5lmr - Revision history

OCA at 18:35, 18 October 2023

OCA — Wed, 18 Oct 2023 18:35:05 GMT

←Older revision		Revision as of 18:35, 18 October 2023
Line 3:		Line 3:
	<SX load='5lmr' size='340' side='right' viewer='molstar' caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>		<SX load='5lmr' size='340' side='right' viewer='molstar' caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lmr]] is a 25 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8~~ Thermus thermophilus ~~hb8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5LMR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lmr]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LMR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 4.45Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">infA, TTHA1669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), infC, TTHA0551 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=5lmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmr OCA], [https://pdbe.org/5lmr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lmr RCSB], [https://www.ebi.ac.uk/pdbsum/5lmr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmr ProSAT]</span></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=5lmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmr OCA], [~~http~~://pdbe.org/5lmr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lmr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lmr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmr ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]	+	[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5lmr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5lmr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 27:
	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Thermus thermophilus ~~hb8]]~~	+	[[Category: Thermus thermophilus HB8]]
-	~~[[Category: Thet8~~]]	+	[[Category: Hussain T]]
-	[[Category: Hussain, T]]	+	[[Category: Llacer JL]]
-	[[Category: Llacer~~, J L~~]]	+	[[Category: Ramakrishnan V]]
-	[[Category: Ramakrishnan, V]]	+	[[Category: Wimberly BT]]
-	[[Category: Wimberly~~, B T]]~~	+
-	~~[[Category: If1]]~~	+
-	~~[[Category: If3]]~~	+
-	~~[[Category: Initiation factor]]~~	+
-	~~[[Category: Pic]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Thermus thermophilus]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Trnai~~]]	+

OCA at 20:43, 10 April 2020

OCA — Fri, 10 Apr 2020 20:43:51 GMT

←Older revision		Revision as of 20:43, 10 April 2020
Line 3:		Line 3:
	<SX load='5lmr' size='340' side='right' viewer='molstar' caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>		<SX load='5lmr' size='340' side='right' viewer='molstar' caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lmr]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LMR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lmr]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LMR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">infA, TTHA1669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), infC, TTHA0551 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">infA, TTHA1669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), infC, TTHA0551 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=5lmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmr OCA], [http://pdbe.org/5lmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmr RCSB], [http://www.ebi.ac.uk/pdbsum/5lmr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmr ProSAT]</span></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=5lmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmr OCA], [http://pdbe.org/5lmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmr RCSB], [http://www.ebi.ac.uk/pdbsum/5lmr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 18:58, 6 March 2020

OCA — Fri, 06 Mar 2020 18:58:56 GMT

←Older revision		Revision as of 18:58, 6 March 2020
Line 1:		Line 1:

	==Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)==		==Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)==
-	<~~StructureSection~~ load='5lmr' size='340' side='right'caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>	+	<SX load='5lmr' size='340' side='right' viewer='molstar' caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5lmr]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5lmr]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMR FirstGlance]. <br>
Line 10:		Line 10:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345~~] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B~~] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. ~~[[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385]~~ [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531~~] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508~~] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]	+	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5lmr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5lmr" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ribosomal protein THX\|Ribosomal protein THX]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermus thermophilus hb8]]		[[Category: Thermus thermophilus hb8]]

OCA at 10:53, 2 October 2019

OCA — Wed, 02 Oct 2019 10:53:44 GMT

←Older revision		Revision as of 10:53, 2 October 2019
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	==Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)==		==Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)==
-	<StructureSection load='5lmr' size='340' side='right' caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>	+	<StructureSection load='5lmr' size='340' side='right'caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lmr]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lmr]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">infA, TTHA1669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), infC, TTHA0551 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=5lmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmr OCA], [http://pdbe.org/5lmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmr RCSB], [http://www.ebi.ac.uk/pdbsum/5lmr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmr 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=5lmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmr OCA], [http://pdbe.org/5lmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmr RCSB], [http://www.ebi.ac.uk/pdbsum/5lmr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B~~] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B~~] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315~~] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385~~] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B~~] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508~~] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]	+	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5lmr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5lmr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosomal protein THX\|Ribosomal protein THX]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thermus thermophilus hb8]]		[[Category: Thermus thermophilus hb8]]
		+	[[Category: Thet8]]
	[[Category: Hussain, T]]		[[Category: Hussain, T]]
	[[Category: Llacer, J L]]		[[Category: Llacer, J L]]

OCA at 03:28, 16 November 2017

OCA — Thu, 16 Nov 2017 03:28:56 GMT

←Older revision		Revision as of 03:28, 16 November 2017
Line 9:		Line 9:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345~~] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B~~] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. ~~[[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385]~~ [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531~~] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508~~] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]	+	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 04:17, 4 August 2017

OCA — Fri, 04 Aug 2017 04:17:42 GMT

←Older revision		Revision as of 04:17, 4 August 2017
Line 9:		Line 9:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B~~] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B~~] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315~~] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385~~] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B~~] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508~~] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]	+	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 21:38, 5 October 2016

OCA — Wed, 05 Oct 2016 21:38:09 GMT

←Older revision		Revision as of 21:38, 5 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5lmr is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)==
		+	<StructureSection load='5lmr' size='340' side='right' caption='[[5lmr]], [[Resolution\|resolution]] 4.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5lmr]] is a 25 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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=5lmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmr OCA], [http://pdbe.org/5lmr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmr RCSB], [http://www.ebi.ac.uk/pdbsum/5lmr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmr ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/IF1_THET8 IF1_THET8]] One of the essential components for the initiation of protein synthesis. Binds in the vicinity of the A-site (ECO:0000269\|PubMed:11228145). Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex.[HAMAP-Rule:MF_00075]<ref>PMID:11228145</ref> [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/IF3_THET8 IF3_THET8]] IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] 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_B] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition.

-	~~Authors: Hussain~~, T., Llacer~~, J.L.~~, Wimberly, ~~B.T.~~, Ramakrishnan, V.	+	Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.,Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V Cell. 2016 Sep 22;167(1):133-144.e13. doi: 10.1016/j.cell.2016.08.074. PMID:27662086<ref>PMID:27662086</ref>

-	~~Description: Structure~~ of ~~bacterial 30S~~-~~IF1~~-~~IF3-mRNA-tRNA translation pre-initiation complex(state-2B)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5lmr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Thermus thermophilus hb8]]
	[[Category: Hussain, T]]		[[Category: Hussain, T]]
-	~~[[Category: Wimberly, B.T]]~~	+	[[Category: Llacer, J L]]
-	[[Category: Llacer, J.L]]	+
	[[Category: Ramakrishnan, V]]		[[Category: Ramakrishnan, V]]
		+	[[Category: Wimberly, B T]]
		+	[[Category: If1]]
		+	[[Category: If3]]
		+	[[Category: Initiation factor]]
		+	[[Category: Pic]]
		+	[[Category: Ribosome]]
		+	[[Category: Thermus thermophilus]]
		+	[[Category: Translation]]
		+	[[Category: Trnai]]

OCA at 15:02, 9 September 2016

OCA — Fri, 09 Sep 2016 15:02:39 GMT

←Older revision		Revision as of 15:02, 9 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5lmr is ON HOLD	+	The entry 5lmr is ON HOLD until Paper Publication

-	Authors: Hussain, T., Llacer, J.L., Wimberly, B.T., Ramakrishnan, V	+	Authors: Hussain, T., Llacer, J.L., Wimberly, B.T., Ramakrishnan, V.

	Description: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)		Description: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)

OCA: Protected "5lmr" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2016 14:39:49 GMT

Protected "5lmr" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:39, 10 August 2016

OCA: New page: '''Unreleased structure''' The entry 5lmr is ON HOLD Authors: Hussain, T., Llacer, J.L., Wimberly, B.T., Ramakrishnan, V Description: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA trans...

OCA — Wed, 10 Aug 2016 14:39:47 GMT

New page: '''Unreleased structure''' The entry 5lmr is ON HOLD Authors: Hussain, T., Llacer, J.L., Wimberly, B.T., Ramakrishnan, V Description: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA trans...

New page

'''Unreleased structure'''

The entry 5lmr is ON HOLD

Authors: Hussain, T., Llacer, J.L., Wimberly, B.T., Ramakrishnan, V

Description: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)
[[Category: Unreleased Structures]]
[[Category: Hussain, T]]
[[Category: Wimberly, B.T]]
[[Category: Llacer, J.L]]
[[Category: Ramakrishnan, V]]