6w21 - Revision history

OCA at 14:41, 6 March 2024

OCA — Wed, 06 Mar 2024 14:41:14 GMT

←Older revision		Revision as of 14:41, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='6w21' size='340' side='right'caption='[[6w21]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6w21' size='340' side='right'caption='[[6w21]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6w21]] is a 21 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~], [~~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=6W21 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6W21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w21]] is a 21 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [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=6W21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W21 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]] 3.3Å</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]), clpP, A1WS_00920 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=6w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w21 OCA], [https://pdbe.org/6w21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w21 RCSB], [https://www.ebi.ac.uk/pdbsum/6w21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w21 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92]~~ </~~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=6w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w21 OCA], [~~http~~://pdbe.org/6w21 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w21 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w21 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w21 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. [[http://www.uniprot.org/uniprot/S1IIE7_ECOLX S1IIE7_ECOLX]] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.~~[HAMAP-Rule:MF_00444][RuleBase:RU000550][SAAS:SAAS00674840]~~	+	[https://www.uniprot.org/uniprot/CLPP_ECOLI CLPP_ECOLI] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. May play the role of a master protease which is attracted to different substrates by different specificity factors such as ClpA or ClpX.
-	~~<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 6w21" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Ecoli]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Endopeptidase Clp~~]]	+
	[[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 07:39, 27 May 2020

OCA — Wed, 27 May 2020 07:39:27 GMT

←Older revision		Revision as of 07:39, 27 May 2020
Line 1:		Line 1:

	==ClpAP Engaged2 State bound to RepA-GFP==		==ClpAP Engaged2 State bound to RepA-GFP==
-	<StructureSection load='6w21' size='340' side='right'caption='[[6w21]]' scene=''>	+	<StructureSection load='6w21' size='340' side='right'caption='[[6w21]], [[Resolution\|resolution]] 3.30Å' 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=6W21 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w21]] is a 21 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895], [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=6W21 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W21 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=6w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w21 OCA], [http://pdbe.org/6w21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w21 RCSB], [http://www.ebi.ac.uk/pdbsum/6w21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w21 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]), clpP, A1WS_00920 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </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=6w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w21 OCA], [http://pdbe.org/6w21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w21 RCSB], [http://www.ebi.ac.uk/pdbsum/6w21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w21 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. [[http://www.uniprot.org/uniprot/S1IIE7_ECOLX S1IIE7_ECOLX]] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.[HAMAP-Rule:MF_00444][RuleBase:RU000550][SAAS:SAAS00674840]
		+	<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 6w21" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Ecoli]]
		+	[[Category: Endopeptidase Clp]]
	[[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 05:35, 13 May 2020

OCA — Wed, 13 May 2020 05:35:58 GMT

←Older revision		Revision as of 05:35, 13 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6w21 ~~is ON HOLD~~	+	==ClpAP Engaged2 State bound to RepA-GFP==
-		+	<StructureSection load='6w21' size='340' side='right'caption='[[6w21]]' 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=6W21 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W21 FirstGlance]. <br>
-	~~Description: ClpAP Engaged2 State bound to RepA-GFP~~	+	</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=6w21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w21 OCA], [http://pdbe.org/6w21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w21 RCSB], [http://www.ebi.ac.uk/pdbsum/6w21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w21 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Thwin, A.C~~]]	+	__TOC__
-	[[Category: ~~Rizo, A.N~~]]	+	</StructureSection>
-	[[Category: Lucius~~, A.L~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Southworth, D.R~~]]	+	[[Category: Lin J]]
-	[[Category: ~~Lin, J~~]]	+	[[Category: Lopez KL]]
-	[[Category: Shorter, J]]	+	[[Category: Lucius AL]]
-	[[Category: ~~Tse, E~~]]	+	[[Category: Rizo AN]]
-	[[Category: ~~Lopez, K.L~~]]	+	[[Category: Scull NW]]
-	[[Category: ~~Scull, N.W~~]]	+	[[Category: Shorter J]]
		+	[[Category: Southworth DR]]
		+	[[Category: Thwin AC]]
		+	[[Category: Tse E]]

OCA: Protected "6w21" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 06:12:03 GMT

Protected "6w21" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:12, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6w21 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 06:12:01 GMT

New page: '''Unreleased structure''' The entry 6w21 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 6w21 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: ClpAP Engaged2 State bound to RepA-GFP
[[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]]