6wd2 - Revision history

OCA at 14:43, 6 March 2024

OCA — Wed, 06 Mar 2024 14:43:01 GMT

←Older revision		Revision as of 14:43, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='6wd2' size='340' side='right'caption='[[6wd2]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='6wd2' size='340' side='right'caption='[[6wd2]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6wd2]] is a 59 chain structure with sequence from [~~http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895], [http~~://en.wikipedia.org/wiki/Escherichia_coli ~~Escherichia coli] and [http://en.wikipedia.org/wiki/Escherichia_coli_~~ Escherichia coli ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WD2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WD2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wd2]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WD2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.6Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6wd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wd2 OCA], [~~http~~://pdbe.org/6wd2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wd2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wd2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wd2 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene></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=6wd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wd2 OCA], [https://pdbe.org/6wd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wd2 RCSB], [https://www.ebi.ac.uk/pdbsum/6wd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wd2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/L3PZ69_ECOLX L3PZ69_ECOLX]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.[HAMAP-Rule:MF_01306] With S5 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01306] [[http://www.uniprot.org/uniprot/A0A376HTV6_ECOLX A0A376HTV6_ECOLX]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309] [[http://www.uniprot.org/uniprot/D7XH79_ECOLX D7XH79_ECOLX]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00629804] [[http://www.uniprot.org/uniprot/A0A073FNB4_ECOLX A0A073FNB4_ECOLX]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors.[ARBA:ARBA00002633][HAMAP-Rule:MF_00362] [[http://www.uniprot.org/uniprot/D7ZEN7_ECOLX D7ZEN7_ECOLX]] This protein binds to 23S rRNA in the presence of protein L20.[RuleBase:RU000562][SAAS:SAAS00637547] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. 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 highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/D7Z9G0_ECOLX D7Z9G0_ECOLX]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome.[HAMAP-Rule:MF_01331] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g., L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331][RuleBase:RU004008] [[http://www.uniprot.org/uniprot/L3CCT0_ECOLX L3CCT0_ECOLX]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.[HAMAP-Rule:MF_00382][RuleBase:RU000560] [[http://www.uniprot.org/uniprot/D7XN21_ECOLX D7XN21_ECOLX]] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_01343][RuleBase:RU004524] [[http://www.uniprot.org/uniprot/I2UH22_ECOLX I2UH22_ECOLX]] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/D7XKZ6_ECOLX D7XKZ6_ECOLX]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326] 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.[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/F4TL27_ECOLX F4TL27_ECOLX]] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/T6N332_ECOLX T6N332_ECOLX]] Binds directly to 16S ribosomal RNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/U9YFU2_ECOLX U9YFU2_ECOLX]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/S1CG62_ECOLX S1CG62_ECOLX]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360][SAAS:SAAS00348112] [[http://www.uniprot.org/uniprot/A0A037Y8L6_ECOLX A0A037Y8L6_ECOLX]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00124822] [[http://www.uniprot.org/uniprot/F4SQ43_ECOLX F4SQ43_ECOLX]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/A0A1X3KX08_ECOLX A0A1X3KX08_ECOLX]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/A0A080IK26_ECOLX A0A080IK26_ECOLX]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/D7ZI15_ECOLX D7ZI15_ECOLX]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/D7X302_ECOLX D7X302_ECOLX]] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/S1D5F0_ECOLX S1D5F0_ECOLX]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA.[HAMAP-Rule:MF_00480] [[http://www.uniprot.org/uniprot/D7Z9F6_ECOLX D7Z9F6_ECOLX]] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] 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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/A0A4Y8DMK0_ECOLX A0A4Y8DMK0_ECOLX]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/D7ZET0_ECOLX D7ZET0_ECOLX]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366][RuleBase:RU003878][SAAS:SAAS00672061] [[http://www.uniprot.org/uniprot/E2QFJ4_ECOLX E2QFJ4_ECOLX]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] [[http://www.uniprot.org/uniprot/V6FZ95_ECOLX V6FZ95_ECOLX]] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_00403][RuleBase:RU003623] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403][RuleBase:RU003623] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/E0J6I2_ECOLW E0J6I2_ECOLW]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit.[ARBA:ARBA00003369][HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/I2XAW2_ECOLX I2XAW2_ECOLX]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/S1ERR4_ECOLX S1ERR4_ECOLX]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736][RuleBase:RU003979] [[http://www.uniprot.org/uniprot/S1EUW9_ECOLX S1EUW9_ECOLX]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/F4TL26_ECOLX F4TL26_ECOLX]] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[ARBA:ARBA00003093][HAMAP-Rule:MF_01307] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] [[http://www.uniprot.org/uniprot/D8A1L7_ECOMS D8A1L7_ECOMS]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit.[HAMAP-Rule:MF_01302] [[http://www.uniprot.org/uniprot/I2X0X3_ECOLX I2X0X3_ECOLX]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.[ARBA:ARBA00003686][HAMAP-Rule:MF_00537] [[http://www.uniprot.org/uniprot/D6I208_ECOLX D6I208_ECOLX]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/A0A5B7PA13_ECOLX A0A5B7PA13_ECOLX]] 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][RuleBase:RU003870]	+	[https://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. 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 highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B]
-	~~<div style="background-color~~:~~#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by~~ the ~~elongation factor EF-Tu(1)~~. ~~To understand~~ the ~~molecular mechanism~~ of ~~this proofreading step~~ it is ~~necessary to visualize GTP-catalysed elongation, which has remained a challenge(2-4)~~. ~~Here we use time-resolved cryogenic electron microscopy to reveal 33 ribosomal states after the delivery~~ of ~~aminoacyl-tRNA by EF-Tu*GTP. Instead of locking cognate tRNA upon initial recognition,~~ the ~~ribosomal decoding centre dynamically monitors codon-anticodon interactions before~~ and ~~after GTP hydrolysis. GTP hydrolysis enables~~ the ~~GTPase domain of EF-Tu to extend away~~, ~~releasing EF-Tu from~~ tRNA. ~~The 30S subunit then locks cognate tRNA in the decoding centre and rotates, enabling the tRNA~~ to ~~bypass 50S protrusions during accommodation into~~ the ~~peptidyl transferase centre~~. ~~By contrast,~~ the ~~decoding centre fails~~ to ~~lock near-cognate tRNA, enabling~~ the ~~dissociation of near-cognate tRNA both during initial selection~~ (~~before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between ribosomes in initial selection states(5~~,6) ~~and~~ in ~~proofreading states, which together govern~~ the ~~efficient rejection of incorrect tRNA~~.	+

-	Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading.,Loveland AB, Demo G, Korostelev AA Nature. 2020 Aug;584(7822):640-645. doi: 10.1038/s41586-020-2447-x. Epub 2020 Jul, 1. PMID:32612237<ref>PMID:32612237</ref>	+	==See Also==
-		+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6wd2" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus coli migula 1895]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Demo, G]]	+	[[Category: Demo G]]
-	[[Category: Korostelev~~, A A~~]]	+	[[Category: Korostelev AA]]
-	[[Category: Loveland~~, A B]]~~	+	[[Category: Loveland AB]]
-	~~[[Category: Ef-tu]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Ribosome-rna complex]]~~	+
-	~~[[Category: Trna~~]]	+

OCA at 09:57, 9 September 2020

OCA — Wed, 09 Sep 2020 09:57:50 GMT

←Older revision		Revision as of 09:57, 9 September 2020
Line 1:		Line 1:

	==Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-A)==		==Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-A)==
-	<StructureSection load='6wd2' size='340' side='right'caption='[[6wd2]]' scene=''>	+	<StructureSection load='6wd2' size='340' side='right'caption='[[6wd2]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WD2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WD2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wd2]] is a 59 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895], [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Escherichia_coli_ Escherichia coli ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WD2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WD2 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wd2 OCA], [http://pdbe.org/6wd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wd2 RCSB], [http://www.ebi.ac.uk/pdbsum/6wd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wd2 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wd2 OCA], [http://pdbe.org/6wd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wd2 RCSB], [http://www.ebi.ac.uk/pdbsum/6wd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wd2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/L3PZ69_ECOLX L3PZ69_ECOLX]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.[HAMAP-Rule:MF_01306] With S5 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01306] [[http://www.uniprot.org/uniprot/A0A376HTV6_ECOLX A0A376HTV6_ECOLX]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309] [[http://www.uniprot.org/uniprot/D7XH79_ECOLX D7XH79_ECOLX]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00629804] [[http://www.uniprot.org/uniprot/A0A073FNB4_ECOLX A0A073FNB4_ECOLX]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors.[ARBA:ARBA00002633][HAMAP-Rule:MF_00362] [[http://www.uniprot.org/uniprot/D7ZEN7_ECOLX D7ZEN7_ECOLX]] This protein binds to 23S rRNA in the presence of protein L20.[RuleBase:RU000562][SAAS:SAAS00637547] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. 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 highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/D7Z9G0_ECOLX D7Z9G0_ECOLX]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome.[HAMAP-Rule:MF_01331] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g., L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331][RuleBase:RU004008] [[http://www.uniprot.org/uniprot/L3CCT0_ECOLX L3CCT0_ECOLX]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.[HAMAP-Rule:MF_00382][RuleBase:RU000560] [[http://www.uniprot.org/uniprot/D7XN21_ECOLX D7XN21_ECOLX]] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_01343][RuleBase:RU004524] [[http://www.uniprot.org/uniprot/I2UH22_ECOLX I2UH22_ECOLX]] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/D7XKZ6_ECOLX D7XKZ6_ECOLX]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326] 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.[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/F4TL27_ECOLX F4TL27_ECOLX]] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/T6N332_ECOLX T6N332_ECOLX]] Binds directly to 16S ribosomal RNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/U9YFU2_ECOLX U9YFU2_ECOLX]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/S1CG62_ECOLX S1CG62_ECOLX]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360][SAAS:SAAS00348112] [[http://www.uniprot.org/uniprot/A0A037Y8L6_ECOLX A0A037Y8L6_ECOLX]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00124822] [[http://www.uniprot.org/uniprot/F4SQ43_ECOLX F4SQ43_ECOLX]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/A0A1X3KX08_ECOLX A0A1X3KX08_ECOLX]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/A0A080IK26_ECOLX A0A080IK26_ECOLX]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/D7ZI15_ECOLX D7ZI15_ECOLX]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/D7X302_ECOLX D7X302_ECOLX]] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/S1D5F0_ECOLX S1D5F0_ECOLX]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA.[HAMAP-Rule:MF_00480] [[http://www.uniprot.org/uniprot/D7Z9F6_ECOLX D7Z9F6_ECOLX]] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] 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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/A0A4Y8DMK0_ECOLX A0A4Y8DMK0_ECOLX]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/D7ZET0_ECOLX D7ZET0_ECOLX]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366][RuleBase:RU003878][SAAS:SAAS00672061] [[http://www.uniprot.org/uniprot/E2QFJ4_ECOLX E2QFJ4_ECOLX]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] [[http://www.uniprot.org/uniprot/V6FZ95_ECOLX V6FZ95_ECOLX]] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_00403][RuleBase:RU003623] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403][RuleBase:RU003623] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/E0J6I2_ECOLW E0J6I2_ECOLW]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit.[ARBA:ARBA00003369][HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/I2XAW2_ECOLX I2XAW2_ECOLX]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/S1ERR4_ECOLX S1ERR4_ECOLX]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736][RuleBase:RU003979] [[http://www.uniprot.org/uniprot/S1EUW9_ECOLX S1EUW9_ECOLX]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/F4TL26_ECOLX F4TL26_ECOLX]] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[ARBA:ARBA00003093][HAMAP-Rule:MF_01307] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] [[http://www.uniprot.org/uniprot/D8A1L7_ECOMS D8A1L7_ECOMS]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit.[HAMAP-Rule:MF_01302] [[http://www.uniprot.org/uniprot/I2X0X3_ECOLX I2X0X3_ECOLX]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.[ARBA:ARBA00003686][HAMAP-Rule:MF_00537] [[http://www.uniprot.org/uniprot/D6I208_ECOLX D6I208_ECOLX]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/A0A5B7PA13_ECOLX A0A5B7PA13_ECOLX]] 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][RuleBase:RU003870]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu(1). To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation, which has remained a challenge(2-4). Here we use time-resolved cryogenic electron microscopy to reveal 33 ribosomal states after the delivery of aminoacyl-tRNA by EF-Tu*GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding centre dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis enables the GTPase domain of EF-Tu to extend away, releasing EF-Tu from tRNA. The 30S subunit then locks cognate tRNA in the decoding centre and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase centre. By contrast, the decoding centre fails to lock near-cognate tRNA, enabling the dissociation of near-cognate tRNA both during initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between ribosomes in initial selection states(5,6) and in proofreading states, which together govern the efficient rejection of incorrect tRNA.
		+
		+	Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading.,Loveland AB, Demo G, Korostelev AA Nature. 2020 Aug;584(7822):640-645. doi: 10.1038/s41586-020-2447-x. Epub 2020 Jul, 1. PMID:32612237<ref>PMID:32612237</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6wd2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Demo G]]	+	[[Category: Demo, G]]
-	[[Category: Korostelev AA]]	+	[[Category: Korostelev, A A]]
-	[[Category: Loveland AB]]	+	[[Category: Loveland, A B]]
		+	[[Category: Ef-tu]]
		+	[[Category: Ribosome]]
		+	[[Category: Ribosome-rna complex]]
		+	[[Category: Trna]]

OCA at 14:08, 8 July 2020

OCA — Wed, 08 Jul 2020 14:08:20 GMT

←Older revision		Revision as of 14:08, 8 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6wd2 is ~~ON HOLD~~	+	==Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-A)==
-		+	<StructureSection load='6wd2' size='340' side='right'caption='[[6wd2]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WD2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WD2 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wd2 OCA], [http://pdbe.org/6wd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wd2 RCSB], [http://www.ebi.ac.uk/pdbsum/6wd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wd2 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Demo G]]
		+	[[Category: Korostelev AA]]
		+	[[Category: Loveland AB]]

OCA: Protected "6wd2" [edit=sysop:move=sysop]

OCA — Wed, 08 Apr 2020 05:37:48 GMT

Protected "6wd2" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:37, 8 April 2020

OCA: New page: '''Unreleased structure''' The entry 6wd2 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Apr 2020 05:37:47 GMT

New page: '''Unreleased structure''' The entry 6wd2 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6wd2 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]