6w22 - Revision history

OCA at 14:41, 6 March 2024

OCA — Wed, 06 Mar 2024 14:41:17 GMT

←Older revision		Revision as of 14:41, 6 March 2024
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	<StructureSection load='6w22' size='340' side='right'caption='[[6w22]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6w22' size='340' side='right'caption='[[6w22]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6w22]] is a 7 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~] and [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W22 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6W22 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w22]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W22 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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]] 3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~UNK~~:~~UNKNOWN~~'>~~UNK~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">clpA, lopD, b0882, JW0866 ([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=6w22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w22 OCA], [https://pdbe.org/6w22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w22 RCSB], [https://www.ebi.ac.uk/pdbsum/6w22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w22 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=6w22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w22 OCA], [~~http~~://pdbe.org/6w22 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w22 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w22 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w22 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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.	+	[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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli ClpAP undergoing active substrate unfolding and proteolysis. A spiral of pore loop-substrate contacts spans both ClpA AAA+ domains. Protomers at the spiral seam undergo nucleotide-specific rearrangements, supporting substrate translocation. IGL loops extend flexibly to bind the planar, heptameric ClpP surface with the empty, symmetry-mismatched IGL pocket maintained at the seam. Three different structures identify a binding-pocket switch by the IGL loop of the lowest positioned protomer, involving release and re-engagement with the clockwise pocket. This switch is coupled to a ClpA rotation and a network of conformational changes across the seam, suggesting that ClpA can rotate around the ClpP apical surface during processive steps of translocation and proteolysis.	+

-	Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis.,Lopez KE, Rizo AN, Tse E, Lin J, Scull NW, Thwin AC, Lucius AL, Shorter J, Southworth DR Nat Struct Mol Biol. 2020 Apr 20. pii: 10.1038/s41594-020-0409-5. doi:, 10.1038/s41594-020-0409-5. PMID:32313240<ref>PMID:32313240</ref>	+	==See Also==
-		+	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6w22" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Lin, J]]	+	[[Category: Lin J]]
-	[[Category: Lopez~~, K L~~]]	+	[[Category: Lopez KL]]
-	[[Category: Lucius~~, A L~~]]	+	[[Category: Lucius AL]]
-	[[Category: Rizo~~, A N~~]]	+	[[Category: Rizo AN]]
-	[[Category: Scull~~, N W~~]]	+	[[Category: Scull NW]]
-	[[Category: Shorter, J]]	+	[[Category: Shorter J]]
-	[[Category: Southworth~~, D R~~]]	+	[[Category: Southworth DR]]
-	[[Category: Thwin~~, A C~~]]	+	[[Category: Thwin AC]]
-	[[Category: Tse, E]]	+	[[Category: Tse E]]
-	~~[[Category: Aaa+]]~~	+
-	~~[[Category: Atpase]]~~	+
-	~~[[Category: Chaperone]]~~	+
-	~~[[Category: Hsp100]]~~	+
-	~~[[Category: Protease~~]]	+

OCA at 06:43, 6 May 2020

OCA — Wed, 06 May 2020 06:43:06 GMT

←Older revision		Revision as of 06:43, 6 May 2020
Line 1:		Line 1:

	==ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)==		==ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)==
-	<StructureSection load='6w22' size='340' side='right'caption='[[6w22]]' scene=''>	+	<StructureSection load='6w22' size='340' side='right'caption='[[6w22]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W22 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W22 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w22]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W22 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W22 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6w22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w22 OCA], [http://pdbe.org/6w22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w22 RCSB], [http://www.ebi.ac.uk/pdbsum/6w22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w22 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpA, lopD, b0882, JW0866 ([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://proteopedia.org/fgij/fg.htm?mol=6w22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w22 OCA], [http://pdbe.org/6w22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w22 RCSB], [http://www.ebi.ac.uk/pdbsum/6w22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w22 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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;">
		+	== Publication Abstract from PubMed ==
		+	The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli ClpAP undergoing active substrate unfolding and proteolysis. A spiral of pore loop-substrate contacts spans both ClpA AAA+ domains. Protomers at the spiral seam undergo nucleotide-specific rearrangements, supporting substrate translocation. IGL loops extend flexibly to bind the planar, heptameric ClpP surface with the empty, symmetry-mismatched IGL pocket maintained at the seam. Three different structures identify a binding-pocket switch by the IGL loop of the lowest positioned protomer, involving release and re-engagement with the clockwise pocket. This switch is coupled to a ClpA rotation and a network of conformational changes across the seam, suggesting that ClpA can rotate around the ClpP apical surface during processive steps of translocation and proteolysis.
		+
		+	Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis.,Lopez KE, Rizo AN, Tse E, Lin J, Scull NW, Thwin AC, Lucius AL, Shorter J, Southworth DR Nat Struct Mol Biol. 2020 Apr 20. pii: 10.1038/s41594-020-0409-5. doi:, 10.1038/s41594-020-0409-5. PMID:32313240<ref>PMID:32313240</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6w22" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lin J]]	+	[[Category: Synthetic construct sequences]]
-	[[Category: Lopez KL]]	+	[[Category: Lin, J]]
-	[[Category: Lucius AL]]	+	[[Category: Lopez, K L]]
-	[[Category: Rizo AN]]	+	[[Category: Lucius, A L]]
-	[[Category: Scull NW]]	+	[[Category: Rizo, A N]]
-	[[Category: Shorter J]]	+	[[Category: Scull, N W]]
-	[[Category: Southworth DR]]	+	[[Category: Shorter, J]]
-	[[Category: Thwin AC]]	+	[[Category: Southworth, D R]]
-	[[Category: Tse E]]	+	[[Category: Thwin, A C]]
		+	[[Category: Tse, E]]
		+	[[Category: Aaa+]]
		+	[[Category: Atpase]]
		+	[[Category: Chaperone]]
		+	[[Category: Hsp100]]
		+	[[Category: Protease]]

OCA at 06:48, 29 April 2020

OCA — Wed, 29 Apr 2020 06:48:09 GMT

←Older revision		Revision as of 06:48, 29 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6w22 ~~is ON HOLD~~	+	==ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)==
-		+	<StructureSection load='6w22' size='340' side='right'caption='[[6w22]]' scene=''>
-	~~Authors~~: ~~Lopez, K~~.L.~~, Rizo, A~~.N.~~, Tse, E~~.~~, Lin, J~~.~~, Scull, N~~.W., ~~Thwin, A~~.C., ~~Lucius~~, A.L., ~~Shorter, J~~., ~~Southworth, D~~.R.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W22 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W22 FirstGlance]. <br>
-	~~Description: ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)~~	+	</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=6w22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w22 OCA], [http://pdbe.org/6w22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w22 RCSB], [http://www.ebi.ac.uk/pdbsum/6w22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w22 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Southworth, D.R~~]]	+	__TOC__
-	[[Category: ~~Lin, J~~]]	+	</StructureSection>
-	[[Category: ~~Shorter, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Thwin, A.C~~]]	+	[[Category: Lin J]]
-	[[Category: ~~Tse, E~~]]	+	[[Category: Lopez KL]]
-	[[Category: ~~Lucius, A.L~~]]	+	[[Category: Lucius AL]]
-	[[Category: ~~Scull, N.W~~]]	+	[[Category: Rizo AN]]
-	[[Category: ~~Lopez, K.L~~]]	+	[[Category: Scull NW]]
-	[[Category: ~~Rizo, A.N~~]]	+	[[Category: Shorter J]]
		+	[[Category: Southworth DR]]
		+	[[Category: Thwin AC]]
		+	[[Category: Tse E]]

OCA at 05:19, 15 April 2020

OCA — Wed, 15 Apr 2020 05:19:16 GMT

←Older revision		Revision as of 05:19, 15 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6w22 is ON HOLD ~~until sometime in the future~~	+	The entry 6w22 is ON HOLD

	Authors: Lopez, K.L., Rizo, A.N., Tse, E., Lin, J., Scull, N.W., Thwin, A.C., Lucius, A.L., Shorter, J., Southworth, D.R.		Authors: Lopez, K.L., Rizo, A.N., Tse, E., Lin, J., Scull, N.W., Thwin, A.C., Lucius, A.L., Shorter, J., Southworth, D.R.

OCA at 05:31, 8 April 2020

OCA — Wed, 08 Apr 2020 05:31:44 GMT

←Older revision		Revision as of 05:31, 8 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6w22 is ON HOLD	+	The entry 6w22 is ON HOLD until sometime in the future

	Authors: Lopez, K.L., Rizo, A.N., Tse, E., Lin, J., Scull, N.W., Thwin, A.C., Lucius, A.L., Shorter, J., Southworth, D.R.		Authors: Lopez, K.L., Rizo, A.N., Tse, E., Lin, J., Scull, N.W., Thwin, A.C., Lucius, A.L., Shorter, J., Southworth, D.R.
Line 7:		Line 7:
	Description: ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)		Description: ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Thwin, A.C]]
-	[[Category: Rizo, A.N]]
-	[[Category: Lucius, A.L]]
	[[Category: Southworth, D.R]]		[[Category: Southworth, D.R]]
	[[Category: Lin, J]]		[[Category: Lin, J]]
	[[Category: Shorter, J]]		[[Category: Shorter, J]]
		+	[[Category: Thwin, A.C]]
	[[Category: Tse, E]]		[[Category: Tse, E]]
-	[[Category: ~~Lopez~~, K.L]]	+	[[Category: Lucius, A.L]]
	[[Category: Scull, N.W]]		[[Category: Scull, N.W]]
		+	[[Category: Lopez, K.L]]
		+	[[Category: Rizo, A.N]]

OCA: Protected "6w22" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 06:12:05 GMT

Protected "6w22" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:12, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6w22 is ON HOLD Authors: Lopez, K.L., Rizo, A.N., Tse, E., Lin, J., Scull, N.W., Thwin, A.C., Lucius, A.L., Shorter, J., Southworth, D.R. Descripti...

OCA — Wed, 11 Mar 2020 06:12:04 GMT

New page: '''Unreleased structure''' The entry 6w22 is ON HOLD Authors: Lopez, K.L., Rizo, A.N., Tse, E., Lin, J., Scull, N.W., Thwin, A.C., Lucius, A.L., Shorter, J., Southworth, D.R. Descripti...

New page

'''Unreleased structure'''

The entry 6w22 is ON HOLD

Authors: Lopez, K.L., Rizo, A.N., Tse, E., Lin, J., Scull, N.W., Thwin, A.C., Lucius, A.L., Shorter, J., Southworth, D.R.

Description: ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)
[[Category: Unreleased Structures]]
[[Category: Thwin, A.C]]
[[Category: Rizo, A.N]]
[[Category: Lucius, A.L]]
[[Category: Southworth, D.R]]
[[Category: Lin, J]]
[[Category: Shorter, J]]
[[Category: Tse, E]]
[[Category: Lopez, K.L]]
[[Category: Scull, N.W]]