2otl - Revision history

OCA at 10:48, 30 August 2023

2023-08-30T10:48:20Z

←Older revision		Revision as of 10:48, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2otl' size='340' side='right'caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2otl' size='340' side='right'caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from ~~[https://en.wikipedia.org/wiki/"flavobacterium_(halobacterium)_maris-mortui_(sic)"_elazari-volcani_1940 "flavobacterium (halobacterium) maris-mortui (sic)" elazari-volcani 1940] and~~ [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OTL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2otl]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OTL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA~~</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.7Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA~~</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2otj\|2otj]]</div~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [https://pdbe.org/2otl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [https://www.ebi.ac.uk/pdbsum/2otl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2otl ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [https://pdbe.org/2otl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [https://www.ebi.ac.uk/pdbsum/2otl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2otl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[https://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[https://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[https://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[https://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[https://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[https://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[https://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[https://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[https://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[https://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[https://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[https://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[https://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[https://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[https://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[https://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[https://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[https://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[https://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[https://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[https://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[https://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[https://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[https://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[https://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[https://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]	+	[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 38:
	[[Category: Haloarcula marismortui]]		[[Category: Haloarcula marismortui]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blaha, G]]	+	[[Category: Blaha G]]
-	[[Category: Schroeder~~, S J~~]]	+	[[Category: Schroeder SJ]]
-	[[Category: Tirado-Rives, J]]	+	[[Category: Tirado-Rives J]]
-	~~[[Category: Antibiotic complex]]~~	+
-	~~[[Category: Girodazole]]~~	+
-	~~[[Category: Girolline]]~~	+
-	~~[[Category: Large subunit]]~~	+
-	~~[[Category: Ribosome~~]]	+

OCA at 13:05, 9 June 2021

2021-06-09T13:05:36Z

←Older revision		Revision as of 13:05, 9 June 2021
Line 3:		Line 3:
	<StructureSection load='2otl' size='340' side='right'caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2otl' size='340' side='right'caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_(halobacterium)_maris-mortui_(sic)"_elazari-volcani_1940 "flavobacterium (halobacterium) maris-mortui (sic)" elazari-volcani 1940] and [~~http~~://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OTL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_(halobacterium)_maris-mortui_(sic)"_elazari-volcani_1940 "flavobacterium (halobacterium) maris-mortui (sic)" elazari-volcani 1940] and [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OTL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2otj\|2otj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2otj\|2otj]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [~~http~~://pdbe.org/2otl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2otl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2otl ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [https://pdbe.org/2otl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [https://www.ebi.ac.uk/pdbsum/2otl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2otl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[~~http~~://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[~~http~~://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[~~http~~://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[~~http~~://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[~~http~~://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[~~http~~://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[~~http~~://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[~~http~~://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[~~http~~://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[~~http~~://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[~~http~~://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[~~http~~://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[~~http~~://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[~~http~~://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[~~http~~://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[~~http~~://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[~~http~~://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[~~http~~://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[~~http~~://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[~~http~~://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[~~http~~://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[~~http~~://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[~~http~~://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[~~http~~://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[~~http~~://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[~~http~~://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[~~http~~://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]	+	[[https://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[https://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[https://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[https://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[https://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[https://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[https://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[https://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[https://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[https://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[https://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[https://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[https://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[https://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[https://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[https://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[https://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[https://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[https://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[https://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[https://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[https://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[https://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[https://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[https://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[https://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[https://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:44, 31 July 2019

2019-07-31T07:44:46Z

←Older revision		Revision as of 07:44, 31 July 2019
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Girodazole bound to the large subunit of Haloarcula marismortui==		==Girodazole bound to the large subunit of Haloarcula marismortui==
-	<StructureSection load='2otl' size='340' side='right' caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='2otl' size='340' side='right'caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_(halobacterium)_maris-mortui_(sic)"_elazari-volcani_1940 "flavobacterium (halobacterium) maris-mortui (sic)" elazari-volcani 1940] and [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OTL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_(halobacterium)_maris-mortui_(sic)"_elazari-volcani_1940 "flavobacterium (halobacterium) maris-mortui (sic)" elazari-volcani 1940] and [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OTL FirstGlance]. <br>
Line 9:		Line 9:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://pdbe.org/2otl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2otl ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://pdbe.org/2otl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2otl ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374~~] [[http://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329~~] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/~~RL39_HALMA RL39_HALMA~~]] ~~Binds to~~ the ~~23S~~ rRNA~~. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to~~ the 23S rRNA.[HAMAP-Rule:~~MF_00327~~] [[http://www.uniprot.org/uniprot/~~RL31_HALMA RL31_HALMA~~]] Binds to the 23S rRNA. ~~Located at~~ the polypeptide exit tunnel ~~on the outside of the subunit~~.[HAMAP-Rule:~~MF_00410~~] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367~~] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369~~] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[http://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]	+	[[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[http://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ot/2otl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ot/2otl_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 39:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Haloarcula marismortui]]		[[Category: Haloarcula marismortui]]
		+	[[Category: Large Structures]]
	[[Category: Blaha, G]]		[[Category: Blaha, G]]
	[[Category: Schroeder, S J]]		[[Category: Schroeder, S J]]

OCA at 09:10, 18 October 2017

2017-10-18T09:10:16Z

←Older revision		Revision as of 09:10, 18 October 2017
Line 1:		Line 1:
		+	{{Large structure}}
	==Girodazole bound to the large subunit of Haloarcula marismortui==		==Girodazole bound to the large subunit of Haloarcula marismortui==
	<StructureSection load='2otl' size='340' side='right' caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2otl' size='340' side='right' caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2otj\|2otj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2otj\|2otj]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://pdbe.org/2otl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://pdbe.org/2otl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2otl ProSAT]</span></td></tr>
	</table>		</table>
	{{Large structure}}		{{Large structure}}
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/~~RL18E_HALMA RL18E_HALMA~~]] ~~Stabilizes~~ the ~~tertiary~~ rRNA ~~structure within~~ the 23S rRNA ~~domain (domain II) to which it binds~~.[HAMAP-Rule:~~MF_00329~~] [[http://www.uniprot.org/uniprot/~~RL39_HALMA RL39_HALMA~~]] Binds to the 23S rRNA. ~~Forms part of~~ the polypeptide exit tunnel.[HAMAP-Rule:~~MF_00629~~] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A~~] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369~~] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]	+	[[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[http://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:03, 8 February 2016

2016-02-08T08:03:45Z

←Older revision		Revision as of 08:03, 8 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2otl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:31, 10 September 2015

2015-09-10T09:31:17Z

←Older revision		Revision as of 09:31, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2otl' size='340' side='right' caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2otl' size='340' side='right' caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OTL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_(halobacterium)_maris-mortui_(sic)"_elazari-volcani_1940 "flavobacterium (halobacterium) maris-mortui (sic)" elazari-volcani 1940] and [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OTL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2otj\|2otj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2otj\|2otj]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://pdbe.org/2otl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum]</span></td></tr>
	</table>		</table>
		+	{{Large structure}}
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/~~RL19_HALMA RL19_HALMA~~]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/~~RL44_HALMA RL44_HALMA~~]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[http://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]	+	[[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[http://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2otl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 21:51, 24 December 2014

2014-12-24T21:51:02Z

←Older revision		Revision as of 21:51, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OTL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OTL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2otj\|2otj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2otj\|2otj]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL19_HALMA RL19_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL44_HALMA RL44_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[http://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL37A_HALMA RL37A_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Haloarcula marismortui]]		[[Category: Haloarcula marismortui]]
-	[[Category: Blaha, G.]]	+	[[Category: Blaha, G]]
-	[[Category: Schroeder, S J.]]	+	[[Category: Schroeder, S J]]
-	[[Category: Tirado-Rives, J~~.]]~~	+	[[Category: Tirado-Rives, J]]
-	~~[[Category: 50~~]]	+
	[[Category: Antibiotic complex]]		[[Category: Antibiotic complex]]
	[[Category: Girodazole]]		[[Category: Girodazole]]

OCA at 20:10, 30 September 2014

2014-09-30T20:10:36Z

←Older revision		Revision as of 20:10, 30 September 2014
Line 1:		Line 1:
-	~~{{Large structure}}~~	+	==Girodazole bound to the large subunit of Haloarcula marismortui==
-	~~{{STRUCTURE_2otl~~\| ~~PDB~~=2otl \| ~~SCENE~~= }}	+	<StructureSection load='2otl' size='340' side='right' caption='[[2otl]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	===~~Girodazole bound~~ to the ~~large subunit~~ of ~~Haloarcula marismortui~~===	+	== Structural highlights ==
-	~~{{ABSTRACT_PUBMED_17321546}}~~	+	<table><tr><td colspan='2'>[[2otl]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OTL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GIR:GIRODAZOLE'>GIR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2otj\|2otj]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2otl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2otl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2otl RCSB], [http://www.ebi.ac.uk/pdbsum/2otl PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ot/2otl_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystal structures of the 50 S ribosomal subunit from Haloarcula marismortui complexed with two antibiotics have identified new sites at which antibiotics interact with the ribosome and inhibit protein synthesis. 13-Deoxytedanolide binds to the E site of the 50 S subunit at the same location as the CCA of tRNA, and thus appears to inhibit protein synthesis by competing with deacylated tRNAs for E site binding. Girodazole binds near the E site region, but is somewhat buried and may inhibit tRNA binding by interfering with conformational changes that occur at the E site. The specificity of 13-deoxytedanolide for eukaryotic ribosomes is explained by its extensive interactions with protein L44e, which is an E site component of archaeal and eukaryotic ribosomes, but not of eubacterial ribosomes. In addition, protein L28, which is unique to the eubacterial E site, overlaps the site occupied by 13-deoxytedanolide, precluding its binding to eubacterial ribosomes. Girodazole is specific for eukarytes and archaea because it makes interactions with L15 that are not possible in eubacteria.

-	~~==About this Structure==~~	+	The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole.,Schroeder SJ, Blaha G, Tirado-Rives J, Steitz TA, Moore PB J Mol Biol. 2007 Apr 13;367(5):1471-9. Epub 2007 Feb 7. PMID:17321546<ref>PMID:17321546</ref>
-	~~[[2otl]] is a 30 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2OTL OCA].~~	+

-	~~==See Also==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	*[[Ribosomal protein L10\|Ribosomal protein L10]]	+	</div>
-	*[[Ribosomal protein L11\|Ribosomal protein L11]]	+
-	*[[Ribosomal protein L13\|Ribosomal protein L13]]	+
-	*[[Ribosomal protein L14\|Ribosomal protein L14]]	+
-	*[[Ribosomal protein L19\|Ribosomal protein L19]]	+
-	*[[Ribosomal protein L2\|Ribosomal protein L2]]	+
-	*[[Ribosomal protein L21\|Ribosomal protein L21]]	+
-	*[[Ribosomal protein L3\|Ribosomal protein L3]]	+
-	*[[Ribosomal protein L34\|Ribosomal protein L34]]	+
-	*[[Ribosomal protein L4\|Ribosomal protein L4]]	+
-	*[[Ribosomal protein L5\|Ribosomal protein L5]]	+
-	*[[Ribosomal protein L6\|Ribosomal protein L6]]	+
-	*[[Ribosomal protein L7\|Ribosomal protein L7]]	+

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:017321546~~</~~ref~~><~~references group="xtra"~~/>	+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Haloarcula marismortui]]		[[Category: Haloarcula marismortui]]
	[[Category: Blaha, G.]]		[[Category: Blaha, G.]]

OCA at 08:21, 11 March 2013

2013-03-11T08:21:55Z

←Older revision		Revision as of 08:21, 11 March 2013
Line 1:		Line 1:
-	~~[[Image:2otl.png\|left\|200px]]~~	+	{{Large structure}}
-		+
	{{STRUCTURE_2otl\| PDB=2otl \| SCENE= }}		{{STRUCTURE_2otl\| PDB=2otl \| SCENE= }}
-
	===Girodazole bound to the large subunit of Haloarcula marismortui===		===Girodazole bound to the large subunit of Haloarcula marismortui===
-
	{{ABSTRACT_PUBMED_17321546}}		{{ABSTRACT_PUBMED_17321546}}

OCA at 09:29, 20 October 2012

2012-10-20T09:29:14Z

←Older revision		Revision as of 09:29, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2otl]] is a 30 chain structure of [[Ribosomal protein L10]], [[Ribosomal protein L11]], [[Ribosomal protein L13]], [[Ribosomal protein L14]], [[Ribosomal protein L19]], [[Ribosomal protein L2]], [[Ribosomal protein L21]], [[Ribosomal protein L3]], [[Ribosomal protein L34]], [[Ribosomal protein L4]], [[Ribosomal protein L5]], [[Ribosomal protein L6]] and [[Ribosomal protein L7]] with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA].	+	[[2otl]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OTL OCA].

	==See Also==		==See Also==