5ofo - Revision history

OCA at 16:48, 13 December 2023

2023-12-13T16:48:22Z

←Older revision		Revision as of 16:48, 13 December 2023
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	<SX load='5ofo' size='340' side='right' viewer='molstar' caption='[[5ofo]], [[Resolution\|resolution]] 4.60Å' scene=''>		<SX load='5ofo' size='340' side='right' viewer='molstar' caption='[[5ofo]], [[Resolution\|resolution]] 4.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ofo]] is a 6 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=5OFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OFO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</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]] 4.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5og1\|5og1]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">clpB, htpM, b2592, JW2573 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [https://pdbe.org/5ofo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [https://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo 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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [~~http~~://pdbe.org/5ofo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CLPB_ECOLI CLPB_ECOLI]] 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:10982797</ref> <ref>PMID:12624113</ref> <ref>PMID:14640692</ref>	+	[https://www.uniprot.org/uniprot/CLPB_ECOLI CLPB_ECOLI] 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:10982797</ref> <ref>PMID:12624113</ref> <ref>PMID:14640692</ref> [https://www.uniprot.org/uniprot/CLPA_ECOLI CLPA_ECOLI] ATP-dependent specificity component of the ClpAP protease. It directs the protease to specific substrates. It has unfoldase activity. The primary function of the ClpA-ClpP complex appears to be the degradation of unfolded or abnormal proteins.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bukau, B]]	+	[[Category: Bukau B]]
-	[[Category: Carroni, M]]	+	[[Category: Carroni M]]
-	[[Category: Deville, C]]	+	[[Category: Deville C]]
-	[[Category: Franke~~, K B~~]]	+	[[Category: Franke KB]]
-	[[Category: Mogk, A]]	+	[[Category: Mogk A]]
-	[[Category: Saibil~~, H R~~]]	+	[[Category: Saibil HR]]
-	[[Category: Topf, M]]	+	[[Category: Topf M]]
-	~~[[Category: Aaa]]~~	+
-	~~[[Category: Chaperone]]~~	+
-	~~[[Category: Clpb]]~~	+
-	~~[[Category: Disaggregase~~]]	+

OCA at 21:27, 10 April 2020

2020-04-10T21:27:18Z

←Older revision		Revision as of 21:27, 10 April 2020
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	<SX load='5ofo' size='340' side='right' viewer='molstar' caption='[[5ofo]], [[Resolution\|resolution]] 4.60Å' scene=''>		<SX load='5ofo' size='340' side='right' viewer='molstar' caption='[[5ofo]], [[Resolution\|resolution]] 4.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OFO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5og1\|5og1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5og1\|5og1]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpB, htpM, b2592, JW2573 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpB, htpM, b2592, JW2573 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [http://pdbe.org/5ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [http://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo 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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [http://pdbe.org/5ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [http://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:23, 6 March 2020

2020-03-06T19:23:42Z

←Older revision		Revision as of 19:23, 6 March 2020
Line 1:		Line 1:

	==Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein==		==Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein==
-	<~~StructureSection~~ load='5ofo' size='340' side='right'caption='[[5ofo]], [[Resolution\|resolution]] 4.60Å' scene=''>	+	<SX load='5ofo' size='340' side='right' viewer='molstar' caption='[[5ofo]], [[Resolution\|resolution]] 4.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OFO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OFO FirstGlance]. <br>
Line 26:		Line 26:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Ecoli]]		[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:23, 21 August 2019

2019-08-21T06:23:08Z

←Older revision		Revision as of 06:23, 21 August 2019
Line 1:		Line 1:

	==Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein==		==Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein==
-	<StructureSection load='5ofo' size='340' side='right' caption='[[5ofo]], [[Resolution\|resolution]] 4.60Å' scene=''>	+	<StructureSection load='5ofo' size='340' side='right'caption='[[5ofo]], [[Resolution\|resolution]] 4.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OFO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5og1\|5og1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5og1\|5og1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpB, htpM, b2592, JW2573 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [http://pdbe.org/5ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [http://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo 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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [http://pdbe.org/5ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [http://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5ofo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ofo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Bukau, B]]		[[Category: Bukau, B]]
	[[Category: Carroni, M]]		[[Category: Carroni, M]]

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

2017-08-24T11:05:25Z

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

←Older revision

Revision as of 11:05, 24 August 2017

OCA: New page: ==Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein== == Structural highlights ==
<table><tr><td colspan='2'>[[5ofo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OFO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5og1|5og1]]</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=5ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ofo OCA], [http://pdbe.org/5ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ofo RCSB], [http://www.ebi.ac.uk/pdbsum/5ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ofo ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/CLPB_ECOLI CLPB_ECOLI]] 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:10982797</ref> <ref>PMID:12624113</ref> <ref>PMID:14640692</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'-O-(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.,Deville C, Carroni M, Franke KB, Topf M, Bukau B, Mogk A, Saibil HR Sci Adv. 2017 Aug 4;3(8):e1701726. doi: 10.1126/sciadv.1701726. eCollection 2017 , Aug. PMID:28798962<ref>PMID:28798962</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ofo" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Bukau, B]]
[[Category: Carroni, M]]
[[Category: Deville, C]]
[[Category: Franke, K B]]
[[Category: Mogk, A]]
[[Category: Saibil, H R]]
[[Category: Topf, M]]
[[Category: Aaa]]
[[Category: Chaperone]]
[[Category: Clpb]]
[[Category: Disaggregase]]