5bq6 - Revision history

OCA at 08:28, 27 September 2023

OCA — Wed, 27 Sep 2023 08:28:37 GMT

←Older revision		Revision as of 08:28, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bq6]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BQ6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bq6]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BQ6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EFB:OLIGOMYCIN+B'>EFB</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EFB:OLIGOMYCIN+B'>EFB</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></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=5bq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bq6 OCA], [https://pdbe.org/5bq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bq6 RCSB], [https://www.ebi.ac.uk/pdbsum/5bq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bq6 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=5bq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bq6 OCA], [https://pdbe.org/5bq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bq6 RCSB], [https://www.ebi.ac.uk/pdbsum/5bq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bq6 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:03, 7 June 2023

OCA — Wed, 07 Jun 2023 06:03:32 GMT

←Older revision		Revision as of 06:03, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5bq6' size='340' side='right'caption='[[5bq6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5bq6' size='340' side='right'caption='[[5bq6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bq6]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BQ6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BQ6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bq6]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BQ6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EFB:OLIGOMYCIN+B'>EFB</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EFB:OLIGOMYCIN+B'>EFB</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>~~</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=5bq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bq6 OCA], [https://pdbe.org/5bq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bq6 RCSB], [https://www.ebi.ac.uk/pdbsum/5bq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bq6 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bps\|5bps]], [[5bqa\|5bqa]], [[5bqj\|5bqj]]~~</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=5bq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bq6 OCA], [~~http~~://pdbe.org/5bq6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bq6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bq6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bq6 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ATP9_YEAST ATP9_YEAST]] Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. A homomeric c-ring of probably 10 subunits is part of the complex rotary element.	+	[https://www.uniprot.org/uniprot/ATP9_YEAST ATP9_YEAST] Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. A homomeric c-ring of probably 10 subunits is part of the complex rotary element.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	We report the high-resolution (1.9 A) crystal structure of oligomycin bound to the subunit c(10) ring of the yeast mitochondrial ATP synthase. Oligomycin binds to the surface of the c(10) ring making contact with two neighboring molecules at a position that explains the inhibitory effect on ATP synthesis. The carboxyl side chain of Glu59, which is essential for proton translocation, forms an H-bond with oligomycin via a bridging water molecule but is otherwise shielded from the aqueous environment. The remaining contacts between oligomycin and subunit c are primarily hydrophobic. The amino acid residues that form the oligomycin-binding site are 100% conserved between human and yeast but are widely different from those in bacterial homologs, thus explaining the differential sensitivity to oligomycin. Prior genetics studies suggest that the oligomycin-binding site overlaps with the binding site of other antibiotics, including those effective against Mycobacterium tuberculosis, and thereby frames a common "drug-binding site." We anticipate that this drug-binding site will serve as an effective target for new antibiotics developed by rational design.	+
-		+
-	~~Oligomycin frames a common drug-binding site in the ATP synthase.,Symersky J, Osowski D, Walters DE, Mueller DM Proc Natl Acad Sci U S A. 2012 Aug 6. PMID:22869738<ref>PMID:22869738</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5bq6" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Mueller~~, D M~~]]	+	[[Category: Mueller DM]]
-	[[Category: Symersky, J]]	+	[[Category: Symersky J]]
-	[[Category: Xu, T]]	+	[[Category: Xu T]]
-	~~[[Category: C10 ring]]~~	+
-	~~[[Category: F1fo atp synthase]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Membrane protein-antibiotic complex]]~~	+
-	~~[[Category: Mitochondria]]~~	+
-	~~[[Category: Oligomycin b]]~~	+
-	~~[[Category: Protein-antibiotic complex~~]]	+

OCA at 07:26, 27 November 2019

OCA — Wed, 27 Nov 2019 07:26:15 GMT

←Older revision		Revision as of 07:26, 27 November 2019
Line 1:		Line 1:
		+
	==Structure of the yeast F1FO ATPase C10 ring with oligomycin B==		==Structure of the yeast F1FO ATPase C10 ring with oligomycin B==
-	<StructureSection load='5bq6' size='340' side='right' caption='[[5bq6]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5bq6' size='340' side='right'caption='[[5bq6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bq6]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BQ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BQ6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bq6]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BQ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BQ6 FirstGlance]. <br>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bps\|5bps]], [[5bqa\|5bqa]], [[5bqj\|5bqj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bps\|5bps]], [[5bqa\|5bqa]], [[5bqj\|5bqj]]</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=5bq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bq6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5bq6 RCSB], [http://www.ebi.ac.uk/pdbsum/5bq6 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=5bq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bq6 OCA], [http://pdbe.org/5bq6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bq6 RCSB], [http://www.ebi.ac.uk/pdbsum/5bq6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bq6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 5bq6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Mueller, D M]]		[[Category: Mueller, D M]]

OCA at 13:27, 26 August 2015

OCA — Wed, 26 Aug 2015 13:27:28 GMT

←Older revision		Revision as of 13:27, 26 August 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of the yeast F1FO ATPase C10 ring with oligomycin B==
		+	<StructureSection load='5bq6' size='340' side='right' caption='[[5bq6]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5bq6]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BQ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BQ6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EFB:OLIGOMYCIN+B'>EFB</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5bps\|5bps]], [[5bqa\|5bqa]], [[5bqj\|5bqj]]</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=5bq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bq6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5bq6 RCSB], [http://www.ebi.ac.uk/pdbsum/5bq6 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ATP9_YEAST ATP9_YEAST]] Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. A homomeric c-ring of probably 10 subunits is part of the complex rotary element.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report the high-resolution (1.9 A) crystal structure of oligomycin bound to the subunit c(10) ring of the yeast mitochondrial ATP synthase. Oligomycin binds to the surface of the c(10) ring making contact with two neighboring molecules at a position that explains the inhibitory effect on ATP synthesis. The carboxyl side chain of Glu59, which is essential for proton translocation, forms an H-bond with oligomycin via a bridging water molecule but is otherwise shielded from the aqueous environment. The remaining contacts between oligomycin and subunit c are primarily hydrophobic. The amino acid residues that form the oligomycin-binding site are 100% conserved between human and yeast but are widely different from those in bacterial homologs, thus explaining the differential sensitivity to oligomycin. Prior genetics studies suggest that the oligomycin-binding site overlaps with the binding site of other antibiotics, including those effective against Mycobacterium tuberculosis, and thereby frames a common "drug-binding site." We anticipate that this drug-binding site will serve as an effective target for new antibiotics developed by rational design.

-	~~The entry 5bq6 is ON HOLD until Paper Publication~~	+	Oligomycin frames a common drug-binding site in the ATP synthase.,Symersky J, Osowski D, Walters DE, Mueller DM Proc Natl Acad Sci U S A. 2012 Aug 6. PMID:22869738<ref>PMID:22869738</ref>

-	~~Authors: Symersky~~, J.~~, Xu, T~~.~~, Mueller, D.M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Structure of the yeast F1FO ATPase C10 ring with oligomycin B~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: Mueller, D.M]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Mueller, D M]]
		+	[[Category: Symersky, J]]
	[[Category: Xu, T]]		[[Category: Xu, T]]
-	[[Category: ~~Symersky, J~~]]	+	[[Category: C10 ring]]
		+	[[Category: F1fo atp synthase]]
		+	[[Category: Membrane]]
		+	[[Category: Membrane protein-antibiotic complex]]
		+	[[Category: Mitochondria]]
		+	[[Category: Oligomycin b]]
		+	[[Category: Protein-antibiotic complex]]

OCA at 12:52, 10 June 2015

OCA — Wed, 10 Jun 2015 12:52:57 GMT

←Older revision		Revision as of 12:52, 10 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5bq6 is ON HOLD	+	The entry 5bq6 is ON HOLD until Paper Publication

	Authors: Symersky, J., Xu, T., Mueller, D.M.		Authors: Symersky, J., Xu, T., Mueller, D.M.

-	Description: ~~STRUCTURE OF THE YEAST~~ F1FO ~~ATPASE~~ C10 ~~RING WITH OLIGOMYCIN~~ B	+	Description: Structure of the yeast F1FO ATPase C10 ring with oligomycin B
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Mueller, D.M]]		[[Category: Mueller, D.M]]
	[[Category: Xu, T]]		[[Category: Xu, T]]
	[[Category: Symersky, J]]		[[Category: Symersky, J]]

OCA: Protected "5bq6" [edit=sysop:move=sysop]

OCA — Wed, 03 Jun 2015 11:48:20 GMT

Protected "5bq6" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:48, 3 June 2015

OCA: New page: '''Unreleased structure''' The entry 5bq6 is ON HOLD Authors: Symersky, J., Xu, T., Mueller, D.M. Description: STRUCTURE OF THE YEAST F1FO ATPASE C10 RING WITH OLIGOMYCIN B [[Category:...

OCA — Wed, 03 Jun 2015 11:48:19 GMT

New page: '''Unreleased structure''' The entry 5bq6 is ON HOLD Authors: Symersky, J., Xu, T., Mueller, D.M. Description: STRUCTURE OF THE YEAST F1FO ATPASE C10 RING WITH OLIGOMYCIN B [[Category:...

New page

'''Unreleased structure'''

The entry 5bq6 is ON HOLD

Authors: Symersky, J., Xu, T., Mueller, D.M.

Description: STRUCTURE OF THE YEAST F1FO ATPASE C10 RING WITH OLIGOMYCIN B
[[Category: Unreleased Structures]]
[[Category: Mueller, D.M]]
[[Category: Xu, T]]
[[Category: Symersky, J]]