1mi6 - Revision history

OCA at 07:44, 14 February 2024

OCA — Wed, 14 Feb 2024 07:44:05 GMT

←Older revision		Revision as of 07:44, 14 February 2024
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	<SX load='1mi6' size='340' side='right' viewer='molstar' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>		<SX load='1mi6' size='340' side='right' viewer='molstar' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Escherichia_coli~~ Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1gqe\|1gqe]]~~, [[~~1dt9~~\|~~1dt9~~]]~~</div>~~</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]] 10.9Å</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=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [https://pdbe.org/1mi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [https://www.ebi.ac.uk/pdbsum/1mi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi6 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [https://pdbe.org/1mi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [https://www.ebi.ac.uk/pdbsum/1mi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RF2_ECOLI RF2_ECOLI]] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.[HAMAP-Rule:MF_00094]	+	[https://www.uniprot.org/uniprot/RF2_ECOLI RF2_ECOLI] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.[HAMAP-Rule:MF_00094]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mi6 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mi6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.
-
-	A cryo-electron microscopic study of ribosome-bound termination factor RF2.,Rawat UB, Zavialov AV, Sengupta J, Valle M, Grassucci RA, Linde J, Vestergaard B, Ehrenberg M, Frank J Nature. 2003 Jan 2;421(6918):87-90. PMID:12511960<ref>PMID:12511960</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1mi6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Escherichia coli]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ehrenberg, M]]	+	[[Category: Ehrenberg M]]
-	[[Category: Frank, J]]	+	[[Category: Frank J]]
-	[[Category: Grassucci~~, R A~~]]	+	[[Category: Grassucci RA]]
-	[[Category: Linde, J]]	+	[[Category: Linde J]]
-	[[Category: Rawat~~, U B.S~~]]	+	[[Category: Rawat UBS]]
-	[[Category: Sengupta, J]]	+	[[Category: Sengupta J]]
-	[[Category: Valle, M]]	+	[[Category: Valle M]]
-	[[Category: Vestergaard, B]]	+	[[Category: Vestergaard B]]
-	[[Category: Zavialov~~, A V]]~~	+	[[Category: Zavialov AV]]
-	~~[[Category: Conformational change]]~~	+
-	~~[[Category: Release complex]]~~	+
-	~~[[Category: Rf2]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 10:15, 12 January 2022

OCA — Wed, 12 Jan 2022 10:15:58 GMT

←Older revision		Revision as of 10:15, 12 January 2022
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	<SX load='1mi6' size='340' side='right' viewer='molstar' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>		<SX load='1mi6' size='340' side='right' viewer='molstar' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gqe\|1gqe]], [[1dt9\|1dt9]]</div></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=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [~~http~~://pdbe.org/1mi6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1mi6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi6 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [https://pdbe.org/1mi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [https://www.ebi.ac.uk/pdbsum/1mi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RF2_ECOLI RF2_ECOLI]] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.[HAMAP-Rule:MF_00094]	+	[[https://www.uniprot.org/uniprot/RF2_ECOLI RF2_ECOLI]] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.[HAMAP-Rule:MF_00094]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:31, 10 April 2020

OCA — Fri, 10 Apr 2020 16:31:19 GMT

←Older revision		Revision as of 16:31, 10 April 2020
Line 3:		Line 3:
	<SX load='1mi6' size='340' side='right' viewer='molstar' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>		<SX load='1mi6' size='340' side='right' viewer='molstar' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</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=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://pdbe.org/1mi6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi6 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=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://pdbe.org/1mi6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 16:46, 6 March 2020

OCA — Fri, 06 Mar 2020 16:46:04 GMT

←Older revision		Revision as of 16:46, 6 March 2020
Line 1:		Line 1:

	==Docking of the modified RF2 X-ray structure into the Low Resolution Cryo-EM map of RF2 E.coli 70S Ribosome==		==Docking of the modified RF2 X-ray structure into the Low Resolution Cryo-EM map of RF2 E.coli 70S Ribosome==
-	<~~StructureSection~~ load='1mi6' size='340' side='right' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>	+	<SX load='1mi6' size='340' side='right' viewer='molstar' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
Line 31:		Line 31:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
	[[Category: Ehrenberg, M]]		[[Category: Ehrenberg, M]]
	[[Category: Frank, J]]		[[Category: Frank, J]]

OCA at 07:46, 18 July 2018

OCA — Wed, 18 Jul 2018 07:46:40 GMT

←Older revision		Revision as of 07:46, 18 July 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mi/1mi6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mi/1mi6_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 10:47, 1 February 2017

OCA — Wed, 01 Feb 2017 10:47:52 GMT

←Older revision		Revision as of 10:47, 1 February 2017
Line 1:		Line 1:
		+
	==Docking of the modified RF2 X-ray structure into the Low Resolution Cryo-EM map of RF2 E.coli 70S Ribosome==		==Docking of the modified RF2 X-ray structure into the Low Resolution Cryo-EM map of RF2 E.coli 70S Ribosome==
	<StructureSection load='1mi6' size='340' side='right' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>		<StructureSection load='1mi6' size='340' side='right' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</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=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://pdbe.org/1mi6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://pdbe.org/1mi6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 23:59, 9 February 2016

OCA — Tue, 09 Feb 2016 23:59:21 GMT

←Older revision		Revision as of 23:59, 9 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mi6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:20, 11 September 2015

OCA — Fri, 11 Sep 2015 03:20:49 GMT

←Older revision		Revision as of 03:20, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</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=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://pdbe.org/1mi6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1mi6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:24, 25 December 2014

OCA — Thu, 25 Dec 2014 10:24:47 GMT

←Older revision		Revision as of 10:24, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RF2_ECOLI RF2_ECOLI]] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.[HAMAP-Rule:MF_00094]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ehrenberg, M]]		[[Category: Ehrenberg, M]]
-	[[Category: Frank, J.]]	+	[[Category: Frank, J]]
-	[[Category: Grassucci, R A.]]	+	[[Category: Grassucci, R A]]
-	[[Category: Linde, J.]]	+	[[Category: Linde, J]]
-	[[Category: Rawat, U B.S.]]	+	[[Category: Rawat, U B.S]]
-	[[Category: Sengupta, J.]]	+	[[Category: Sengupta, J]]
-	[[Category: Valle, M.]]	+	[[Category: Valle, M]]
-	[[Category: Vestergaard, B.]]	+	[[Category: Vestergaard, B]]
-	[[Category: Zavialov, A V.]]	+	[[Category: Zavialov, A V]]
	[[Category: Conformational change]]		[[Category: Conformational change]]
	[[Category: Release complex]]		[[Category: Release complex]]

OCA at 17:01, 28 September 2014

OCA — Sun, 28 Sep 2014 17:01:25 GMT

←Older revision		Revision as of 17:01, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1mi6.~~png~~\|~~left~~\|200px]]	+	==Docking of the modified RF2 X-ray structure into the Low Resolution Cryo-EM map of RF2 E.coli 70S Ribosome==
		+	<StructureSection load='1mi6' size='340' side='right' caption='[[1mi6]], [[Resolution\|resolution]] 10.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqe\|1gqe]], [[1dt9\|1dt9]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [http://www.ebi.ac.uk/pdbsum/1mi6 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mi/1mi6_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.

-	~~{{STRUCTURE_1mi6\| PDB=1mi6 \| SCENE= }}~~	+	A cryo-electron microscopic study of ribosome-bound termination factor RF2.,Rawat UB, Zavialov AV, Sengupta J, Valle M, Grassucci RA, Linde J, Vestergaard B, Ehrenberg M, Frank J Nature. 2003 Jan 2;421(6918):87-90. PMID:12511960<ref>PMID:12511960</ref>

-	~~===Docking~~ of the ~~modified RF2 X-ray structure into the Low Resolution Cryo-EM map~~ of ~~RF2 E~~.~~coli 70S Ribosome===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12511960}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1mi6]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012511960<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ehrenberg, M]]		[[Category: Ehrenberg, M]]