1qvr - Revision history

OCA at 08:18, 14 February 2024

2024-02-14T08:18:15Z

←Older revision		Revision as of 08:18, 14 February 2024
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	<StructureSection load='1qvr' size='340' side='right'caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1qvr' size='340' side='right'caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1QVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QVR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID~~-~~ADENYLATE+ESTER'>ANP</scene>~~, ~~<scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CLPB ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [~~http~~://pdbe.org/1qvr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qvr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qvr 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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [https://pdbe.org/1qvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [https://www.ebi.ac.uk/pdbsum/1qvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qvr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CLPB_THET8 CLPB_THET8]] Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.<ref>PMID:10377389</ref>	+	[https://www.uniprot.org/uniprot/CLPB_THET8 CLPB_THET8] Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.<ref>PMID:10377389</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1qvr 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=1qvr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Molecular chaperones assist protein folding by facilitating their "forward" folding and preventing aggregation. However, once aggregates have formed, these chaperones cannot facilitate protein disaggregation. Bacterial ClpB and its eukaryotic homolog Hsp104 are essential proteins of the heat-shock response, which have the remarkable capacity to rescue stress-damaged proteins from an aggregated state. We have determined the structure of Thermus thermophilus ClpB (TClpB) using a combination of X-ray crystallography and cryo-electron microscopy (cryo-EM). Our single-particle reconstruction shows that TClpB forms a two-tiered hexameric ring. The ClpB/Hsp104-linker consists of an 85 A long and mobile coiled coil that is located on the outside of the hexamer. Our mutagenesis and biochemical data show that both the relative position and motion of this coiled coil are critical for chaperone function. Taken together, we propose a mechanism by which an ATP-driven conformational change is coupled to a large coiled-coil motion, which is indispensable for protein disaggregation.
-
-	The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state.,Lee S, Sowa ME, Watanabe YH, Sigler PB, Chiu W, Yoshida M, Tsai FT Cell. 2003 Oct 17;115(2):229-40. PMID:14567920<ref>PMID:14567920</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qvr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
		+	*[[Chaperone protein ClpB\|Chaperone protein ClpB]]
	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]		*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
		+	*[[3D structures of ClpB\|3D structures of ClpB]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chiu, W]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Lee, S]]	+	[[Category: Chiu W]]
-	[[Category: Sigler~~, P B~~]]	+	[[Category: Lee S]]
-	[[Category: Sowa~~, M E~~]]	+	[[Category: Sigler PB]]
-	[[Category: Tsai~~, F T.F~~]]	+	[[Category: Sowa ME]]
-	[[Category: Watanabe, Y]]	+	[[Category: Tsai FTF]]
-	[[Category: Yoshida, M]]	+	[[Category: Watanabe Y]]
-	~~[[Category: Aaa atpase]]~~	+	[[Category: Yoshida M]]
-	~~[[Category: Chaperone]]~~	+
-	~~[[Category: Coiled coil~~]]	+

OCA at 13:12, 16 December 2020

2020-12-16T13:12:11Z

←Older revision		Revision as of 13:12, 16 December 2020
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	==Crystal Structure Analysis of ClpB==		==Crystal Structure Analysis of ClpB==
-	<StructureSection load='1qvr' size='340' side='right' caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1qvr' size='340' side='right'caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1QVR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://pdbe.org/1qvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qvr 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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://pdbe.org/1qvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qvr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Heat Shock ~~Proteins~~\|Heat Shock ~~Proteins~~]]	+	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Chiu, W]]		[[Category: Chiu, W]]
	[[Category: Lee, S]]		[[Category: Lee, S]]

OCA at 08:08, 28 February 2018

2018-02-28T08:08:21Z

←Older revision		Revision as of 08:08, 28 February 2018
Line 1:		Line 1:
		+
	==Crystal Structure Analysis of ClpB==		==Crystal Structure Analysis of ClpB==
	<StructureSection load='1qvr' size='340' side='right' caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1qvr' size='340' side='right' caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://pdbe.org/1qvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr 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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://pdbe.org/1qvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qvr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qv/1qvr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qv/1qvr_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>
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	[[Category: Aaa atpase]]		[[Category: Aaa atpase]]
	[[Category: Chaperone]]		[[Category: Chaperone]]
		+	[[Category: Coiled coil]]

OCA at 22:49, 9 February 2016

2016-02-09T22:49:02Z

←Older revision		Revision as of 22:49, 9 February 2016
Line 17:		Line 17:
	<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=1qvr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:49, 11 September 2015

2015-09-11T02:49:09Z

←Older revision		Revision as of 02:49, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1qvr' size='340' side='right' caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1qvr' size='340' side='right' caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QVR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 ~~Thermus thermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr 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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://pdbe.org/1qvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1qvr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Heat Shock Proteins\|Heat Shock Proteins]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Chiu, W]]		[[Category: Chiu, W]]
	[[Category: Lee, S]]		[[Category: Lee, S]]

OCA at 10:04, 25 December 2014

2014-12-25T10:04:36Z

←Older revision		Revision as of 10:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QVR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QVR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr 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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CLPB_THET8 CLPB_THET8]] Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK.<ref>PMID:10377389</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Chiu, W.]]	+	[[Category: Chiu, W]]
-	[[Category: Lee, S.]]	+	[[Category: Lee, S]]
-	[[Category: Sigler, P B.]]	+	[[Category: Sigler, P B]]
-	[[Category: Sowa, M E.]]	+	[[Category: Sowa, M E]]
-	[[Category: Tsai, F T.F.]]	+	[[Category: Tsai, F T.F]]
-	[[Category: Watanabe, Y.]]	+	[[Category: Watanabe, Y]]
-	[[Category: Yoshida, M.]]	+	[[Category: Yoshida, M]]
	[[Category: Aaa atpase]]		[[Category: Aaa atpase]]
	[[Category: Chaperone]]		[[Category: Chaperone]]

OCA at 16:39, 29 September 2014

2014-09-29T16:39:57Z

←Older revision		Revision as of 16:39, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1qvr.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure Analysis of ClpB==
		+	<StructureSection load='1qvr' size='340' side='right' caption='[[1qvr]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qvr]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QVR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=1qvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qvr RCSB], [http://www.ebi.ac.uk/pdbsum/1qvr 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/qv/1qvr_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 ==
		+	Molecular chaperones assist protein folding by facilitating their "forward" folding and preventing aggregation. However, once aggregates have formed, these chaperones cannot facilitate protein disaggregation. Bacterial ClpB and its eukaryotic homolog Hsp104 are essential proteins of the heat-shock response, which have the remarkable capacity to rescue stress-damaged proteins from an aggregated state. We have determined the structure of Thermus thermophilus ClpB (TClpB) using a combination of X-ray crystallography and cryo-electron microscopy (cryo-EM). Our single-particle reconstruction shows that TClpB forms a two-tiered hexameric ring. The ClpB/Hsp104-linker consists of an 85 A long and mobile coiled coil that is located on the outside of the hexamer. Our mutagenesis and biochemical data show that both the relative position and motion of this coiled coil are critical for chaperone function. Taken together, we propose a mechanism by which an ATP-driven conformational change is coupled to a large coiled-coil motion, which is indispensable for protein disaggregation.

-	~~{{STRUCTURE_1qvr\| PDB=1qvr \| SCENE= }}~~	+	The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state.,Lee S, Sowa ME, Watanabe YH, Sigler PB, Chiu W, Yoshida M, Tsai FT Cell. 2003 Oct 17;115(2):229-40. PMID:14567920<ref>PMID:14567920</ref>

-	~~===Crystal Structure Analysis~~ of ~~ClpB===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14567920}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1qvr]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:014567920<~~/~~ref~~><~~ref group="xtra">PMID:017009862</ref><references group="xtra"~~/>	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Chiu, W.]]		[[Category: Chiu, W.]]

OCA: Protected "1qvr" [edit=sysop:move=sysop]

2013-01-02T10:01:19Z

Protected "1qvr" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:01, 2 January 2013

OCA at 10:01, 2 January 2013

2013-01-02T10:01:18Z

←Older revision		Revision as of 10:01, 2 January 2013
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-	{{Seed}}
	[[Image:1qvr.png\|left\|200px]]		[[Image:1qvr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1qvr", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1qvr\| PDB=1qvr \| SCENE= }}		{{STRUCTURE_1qvr\| PDB=1qvr \| SCENE= }}

	===Crystal Structure Analysis of ClpB===		===Crystal Structure Analysis of ClpB===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14567920}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14567920 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_14567920}}		{{ABSTRACT_PUBMED_14567920}}

	==About this Structure==		==About this Structure==
-	~~1QVR~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA].	+	[[1qvr]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14567920~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014567920</ref><ref group="xtra">PMID:017009862</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Chiu, W.]]		[[Category: Chiu, W.]]
Line 33:		Line 21:
	[[Category: Yoshida, M.]]		[[Category: Yoshida, M.]]
	[[Category: Aaa atpase]]		[[Category: Aaa atpase]]
-	[[Category: ~~Coiled coil~~]]	+	[[Category: Chaperone]]
-		+
-	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:21:21 2009''~~	+

OCA at 11:21, 17 February 2009

2009-02-17T11:21:23Z

←Older revision		Revision as of 11:21, 17 February 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:1qvr.~~gif~~\|left\|200px]]	+	[[Image:1qvr.png\|left\|200px]]

	<!--		<!--
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1QVR is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA].	+	1QVR is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QVR OCA].

	==Reference==		==Reference==
-	~~The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state., Lee S, Sowa ME, Watanabe YH, Sigler PB, Chiu W, Yoshida M, Tsai FT, Cell. 2003 Oct 17;115(2):229-40.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/14567920 14567920]~~	+	<ref group="xtra">PMID:14567920</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Chiu, W.]]		[[Category: Chiu, W.]]
Line 36:		Line 35:
	[[Category: Coiled coil]]		[[Category: Coiled coil]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 18~~:03:~~17 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:21:21 2009''