6pbs - Revision history

OCA at 07:26, 11 October 2023

OCA — Wed, 11 Oct 2023 07:26:41 GMT

←Older revision		Revision as of 07:26, 11 October 2023
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	<StructureSection load='6pbs' size='340' side='right'caption='[[6pbs]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6pbs' size='340' side='right'caption='[[6pbs]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pbs]] is a 36 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PBS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pbs]] is a 36 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] and [https://en.wikipedia.org/wiki/Nonomuraea_sp._MJM5123 Nonomuraea sp. MJM5123]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PBS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=H14:(2S,3R)-BETA-HYDROXY-PHENYLALANINE'>H14</scene>, <scene name='pdbligand=MLE:N-METHYLLEUCINE'>MLE</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=NZC:N-METHYLIDENE-L-THREONINE'>NZC</scene>, <scene name='pdbligand=O7D:'>O7D</scene>, <scene name='pdbligand=O7G:'>O7G</scene>, <scene name='pdbligand=WZJ:'>WZJ</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=H14:(2S,3R)-BETA-HYDROXY-PHENYLALANINE'>H14</scene>, <scene name='pdbligand=MLE:N-METHYLLEUCINE'>MLE</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=NZC:N-METHYLIDENE-L-THREONINE'>NZC</scene>, <scene name='pdbligand=O7D:4-methoxy-N-methyl-L-tryptophan'>O7D</scene>, <scene name='pdbligand=O7G:N,N-dimethyl-L-valine'>O7G</scene>, <scene name='pdbligand=WZJ:N-methyl-L-alloisoleucine'>WZJ</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpC1, Rv3596c, MTCY07H7B.26 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6pbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbs OCA], [https://pdbe.org/6pbs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pbs RCSB], [https://www.ebi.ac.uk/pdbsum/6pbs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbs 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=6pbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbs OCA], [~~http~~://pdbe.org/6pbs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pbs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pbs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbs ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CLPC1_MYCTU CLPC1_MYCTU]] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP (By similarity). Degrades anti-sigma-E factor RseA in the presence of ClpP2.	+	[https://www.uniprot.org/uniprot/CLPC1_MYCTU CLPC1_MYCTU] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP (By similarity). Degrades anti-sigma-E factor RseA in the presence of ClpP2.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6pbs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6pbs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Clp protease 3D structures\|Clp protease 3D structures]]
		+	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abad-Zapatero, C]]
-	[[Category: Wolf, N M]]
-	[[Category: Atpase]]
-	[[Category: Chaperone-antibiotic complex]]
-	[[Category: Clpc1-ntd]]
-	[[Category: Ecumicin]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Nonomuraea sp. MJM5123]]
		+	[[Category: Abad-Zapatero C]]
		+	[[Category: Wolf NM]]

OCA at 06:55, 30 December 2020

OCA — Wed, 30 Dec 2020 06:55:11 GMT

←Older revision		Revision as of 06:55, 30 December 2020
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	==Structure of ClpC1-NTD in complex with Ecumicin==		==Structure of ClpC1-NTD in complex with Ecumicin==
-	<StructureSection load='6pbs' size='340' side='right'caption='[[6pbs]]' scene=''>	+	<StructureSection load='6pbs' size='340' side='right'caption='[[6pbs]], [[Resolution\|resolution]] 2.50Å' 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=6PBS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PBS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pbs]] is a 36 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PBS 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=6pbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbs OCA], [http://pdbe.org/6pbs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pbs RCSB], [http://www.ebi.ac.uk/pdbsum/6pbs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbs 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=ACT:ACETATE+ION'>ACT</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=H14:(2S,3R)-BETA-HYDROXY-PHENYLALANINE'>H14</scene>, <scene name='pdbligand=MLE:N-METHYLLEUCINE'>MLE</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=NZC:N-METHYLIDENE-L-THREONINE'>NZC</scene>, <scene name='pdbligand=O7D:'>O7D</scene>, <scene name='pdbligand=O7G:'>O7G</scene>, <scene name='pdbligand=WZJ:'>WZJ</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpC1, Rv3596c, MTCY07H7B.26 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6pbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbs OCA], [http://pdbe.org/6pbs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pbs RCSB], [http://www.ebi.ac.uk/pdbsum/6pbs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbs ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CLPC1_MYCTU CLPC1_MYCTU]] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP (By similarity). Degrades anti-sigma-E factor RseA in the presence of ClpP2.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The biological processes related to protein homeostasis in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, have recently been established as critical pathways for therapeutic intervention. Proteins of particular interest are ClpC1 and the ClpC1-ClpP1-ClpP2 proteasome complex. The structure of the potent antituberculosis macrocyclic depsipeptide ecumicin complexed with the N-terminal domain of ClpC1 (ClpC1-NTD) is presented here. Crystals of the ClpC1-NTD-ecumicin complex were monoclinic (unit-cell parameters a = 80.0, b = 130.0, c = 112.0 A, beta = 90.07 degrees ; space group P21; 12 complexes per asymmetric unit) and diffracted to 2.5 A resolution. The structure was solved by molecular replacement using the self-rotation function to resolve space-group ambiguities. The new structure of the ecumicin complex showed a unique 1:2 (target:ligand) stoichiometry exploiting the intramolecular dyad in the alpha-helical fold of the target N-terminal domain. The structure of the ecumicin complex unveiled extensive interactions in the uniquely extended N-terminus, a critical binding site for the known cyclopeptide complexes. This structure, in comparison with the previously reported rufomycin I complex, revealed unique features that could be relevant for understanding the mechanism of action of these potential antituberculosis drug leads. Comparison of the ecumicin complex and the ClpC1-NTD-L92S/L96P double-mutant structure with the available structures of rufomycin I and cyclomarin A complexes revealed a range of conformational changes available to this small N-terminal helical domain and the minor helical alterations involved in the antibiotic-resistance mechanism. The different modes of binding and structural alterations could be related to distinct modes of action.
		+
		+	Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions.,Wolf NM, Lee H, Zagal D, Nam JW, Oh DC, Lee H, Suh JW, Pauli GF, Cho S, Abad-Zapatero C Acta Crystallogr D Struct Biol. 2020 May 1;76(Pt 5):458-471. doi:, 10.1107/S2059798320004027. Epub 2020 Apr 23. PMID:32355042<ref>PMID:32355042</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pbs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abad-Zapatero C]]	+	[[Category: Abad-Zapatero, C]]
-	[[Category: Wolf NM]]	+	[[Category: Wolf, N M]]
		+	[[Category: Atpase]]
		+	[[Category: Chaperone-antibiotic complex]]
		+	[[Category: Clpc1-ntd]]
		+	[[Category: Ecumicin]]
		+	[[Category: Mycobacterium tuberculosis]]

OCA at 05:27, 13 May 2020

OCA — Wed, 13 May 2020 05:27:39 GMT

←Older revision		Revision as of 05:27, 13 May 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6pbs ~~is ON HOLD until Paper Publication~~	+	==Structure of ClpC1-NTD in complex with Ecumicin==
-		+	<StructureSection load='6pbs' size='340' side='right'caption='[[6pbs]]' scene=''>
-	~~Authors~~: ~~Abad~~-~~Zapatero~~, C., ~~Wolf~~, N.M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PBS FirstGlance]. <br>
-	~~Description~~: ~~Structure of ClpC1~~-~~NTD in complex with Ecumicin~~	+	</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=6pbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbs OCA], [http://pdbe.org/6pbs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pbs RCSB], [http://www.ebi.ac.uk/pdbsum/6pbs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbs ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Wolf, N.M~~]]	+	__TOC__
-	[[Category: ~~Abad-Zapatero, C~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Abad-Zapatero C]]
		+	[[Category: Wolf NM]]

OCA at 07:11, 2 October 2019

OCA — Wed, 02 Oct 2019 07:11:00 GMT

←Older revision		Revision as of 07:11, 2 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pbs is ON HOLD	+	The entry 6pbs is ON HOLD until Paper Publication

	Authors: Abad-Zapatero, C., Wolf, N.M.		Authors: Abad-Zapatero, C., Wolf, N.M.

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

OCA — Wed, 26 Jun 2019 05:14:36 GMT

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

←Older revision

Revision as of 05:14, 26 June 2019

OCA: New page: '''Unreleased structure''' The entry 6pbs is ON HOLD Authors: Abad-Zapatero, C., Wolf, N.M. Description: Structure of ClpC1-NTD in complex with Ecumicin [[Category: Unreleased Structur...

OCA — Wed, 26 Jun 2019 05:14:35 GMT

New page: '''Unreleased structure''' The entry 6pbs is ON HOLD Authors: Abad-Zapatero, C., Wolf, N.M. Description: Structure of ClpC1-NTD in complex with Ecumicin [[Category: Unreleased Structur...

New page

'''Unreleased structure'''

The entry 6pbs is ON HOLD

Authors: Abad-Zapatero, C., Wolf, N.M.

Description: Structure of ClpC1-NTD in complex with Ecumicin
[[Category: Unreleased Structures]]
[[Category: Wolf, N.M]]
[[Category: Abad-Zapatero, C]]