6rdk - Revision history

OCA at 10:10, 22 May 2024

OCA — Wed, 22 May 2024 10:10:46 GMT

←Older revision		Revision as of 10:10, 22 May 2024
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	<SX load='6rdk' size='340' side='right' viewer='molstar' caption='[[6rdk]], [[Resolution\|resolution]] 3.70Å' scene=''>		<SX load='6rdk' size='340' side='right' viewer='molstar' caption='[[6rdk]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rdk]] is a 30 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Polytomella_sp.~~_pringsheim_198~~.80 Polytomella sp. ~~pringsheim~~ 198.80]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RDK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6RDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rdk]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Polytomella_sp._Pringsheim_198.80 Polytomella sp. Pringsheim 198.80]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RDK 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.7Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.1.2.2 7.1.2.2] </span></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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rdk OCA], [~~http~~://pdbe.org/6rdk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rdk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rdk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rdk 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=6rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rdk OCA], [https://pdbe.org/6rdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rdk RCSB], [https://www.ebi.ac.uk/pdbsum/6rdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rdk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/A0ZW40_9CHLO A0ZW40_9CHLO]] Produces ATP from ADP in the presence of a proton gradient across the membrane.[RuleBase:RU003551] [[http://www.uniprot.org/uniprot/A0ZW41_9CHLO A0ZW41_9CHLO]] Produces ATP from ADP in the presence of a proton gradient across the membrane.[RuleBase:RU003553]	+	[https://www.uniprot.org/uniprot/A0A5H1ZR95_9CHLO A0A5H1ZR95_9CHLO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6rdk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6rdk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ATPase 3D structures\|ATPase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Polytomella sp. ~~pringsheim~~ 198 80]]	+	[[Category: Polytomella sp. Pringsheim 198 80]]
-	[[Category: Klusch, N]]	+	[[Category: Klusch N]]
-	[[Category: Kuhlbrandt, W]]	+	[[Category: Kuhlbrandt W]]
-	[[Category: Murphy~~, B J~~]]	+	[[Category: Murphy BJ]]
-	[[Category: Yildiz, O]]	+	[[Category: Yildiz O]]
-	~~[[Category: Mitochondrial atp synthase dimer flexible coupling cryoem]]~~	+
-	~~[[Category: Proton transport~~]]	+

OCA at 05:32, 11 April 2020

OCA — Sat, 11 Apr 2020 05:32:26 GMT

←Older revision		Revision as of 05:32, 11 April 2020
Line 3:		Line 3:
	<SX load='6rdk' size='340' side='right' viewer='molstar' caption='[[6rdk]], [[Resolution\|resolution]] 3.70Å' scene=''>		<SX load='6rdk' size='340' side='right' viewer='molstar' caption='[[6rdk]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rdk]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Polytomella_sp._pringsheim_198.80 Polytomella sp. pringsheim 198.80]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RDK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rdk]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Polytomella_sp._pringsheim_198.80 Polytomella sp. pringsheim 198.80]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RDK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RDK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.1.2.2 7.1.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.1.2.2 7.1.2.2] </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=6rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rdk OCA], [http://pdbe.org/6rdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rdk RCSB], [http://www.ebi.ac.uk/pdbsum/6rdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rdk 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=6rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rdk OCA], [http://pdbe.org/6rdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rdk RCSB], [http://www.ebi.ac.uk/pdbsum/6rdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rdk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 00:16, 7 March 2020

OCA — Sat, 07 Mar 2020 00:16:48 GMT

←Older revision		Revision as of 00:16, 7 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, composite map==		==Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, composite map==
-	<~~StructureSection~~ load='6rdk' size='340' side='right'caption='[[6rdk]], [[Resolution\|resolution]] 3.70Å' scene=''>	+	<SX load='6rdk' size='340' side='right' viewer='molstar' caption='[[6rdk]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6rdk]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Polytomella_sp._pringsheim_198.80 Polytomella sp. pringsheim 198.80]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RDK FirstGlance]. <br>		<table><tr><td colspan='2'>[[6rdk]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Polytomella_sp._pringsheim_198.80 Polytomella sp. pringsheim 198.80]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RDK FirstGlance]. <br>
Line 22:		Line 22:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Polytomella sp. pringsheim 198 80]]		[[Category: Polytomella sp. pringsheim 198 80]]

OCA at 06:05, 3 July 2019

OCA — Wed, 03 Jul 2019 06:05:54 GMT

←Older revision		Revision as of 06:05, 3 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6rdk is ~~ON HOLD~~	+	==Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, composite map==
		+	<StructureSection load='6rdk' size='340' side='right'caption='[[6rdk]], [[Resolution\|resolution]] 3.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6rdk]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Polytomella_sp._pringsheim_198.80 Polytomella sp. pringsheim 198.80]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RDK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.1.2.2 7.1.2.2] </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=6rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rdk OCA], [http://pdbe.org/6rdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rdk RCSB], [http://www.ebi.ac.uk/pdbsum/6rdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rdk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0ZW40_9CHLO A0ZW40_9CHLO]] Produces ATP from ADP in the presence of a proton gradient across the membrane.[RuleBase:RU003551] [[http://www.uniprot.org/uniprot/A0ZW41_9CHLO A0ZW41_9CHLO]] Produces ATP from ADP in the presence of a proton gradient across the membrane.[RuleBase:RU003553]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	F1Fo-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy structure of active dimeric ATP synthase from mitochondria of Polytomella sp. at a resolution of 2.7 to 2.8 angstroms. Separation of 13 well-defined rotary substates by three-dimensional classification provides a detailed picture of the molecular motions that accompany c-ring rotation and result in ATP synthesis. Crucially, the F1 head rotates along with the central stalk and c-ring rotor for the first ~30 degrees of each 120 degrees primary rotary step to facilitate flexible coupling of the stoichiometrically mismatched F1 and Fo subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit. A conserved metal ion in the proton access channel may synchronize c-ring protonation with rotation.

-	~~Authors: Murphy, B.J~~., ~~Klusch~~, N., ~~Yildiz~~, O., Kuhlbrandt, W.	+	Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F1-Fo coupling.,Murphy BJ, Klusch N, Langer J, Mills DJ, Yildiz O, Kuhlbrandt W Science. 2019 Jun 21;364(6446). pii: 364/6446/eaaw9128. doi:, 10.1126/science.aaw9128. Epub 2019 Jun 20. PMID:31221832<ref>PMID:31221832</ref>

-	~~Description: Cryo-EM structure~~ of ~~Polytomella F~~-~~ATP synthase, Rotary substate 1B, composite map~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Yildiz, O~~]]	+	<div class="pdbe-citations 6rdk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Polytomella sp. pringsheim 198 80]]
	[[Category: Klusch, N]]		[[Category: Klusch, N]]
	[[Category: Kuhlbrandt, W]]		[[Category: Kuhlbrandt, W]]
-	[[Category: Murphy, B.J]]	+	[[Category: Murphy, B J]]
		+	[[Category: Yildiz, O]]
		+	[[Category: Mitochondrial atp synthase dimer flexible coupling cryoem]]
		+	[[Category: Proton transport]]

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

OCA — Wed, 24 Apr 2019 05:10:51 GMT

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

←Older revision

Revision as of 05:10, 24 April 2019

OCA: New page: '''Unreleased structure''' The entry 6rdk is ON HOLD Authors: Murphy, B.J., Klusch, N., Yildiz, O., Kuhlbrandt, W. Description: Cryo-EM structure of Polytomella F-ATP synthase, Rotary ...

OCA — Wed, 24 Apr 2019 05:10:50 GMT

New page: '''Unreleased structure''' The entry 6rdk is ON HOLD Authors: Murphy, B.J., Klusch, N., Yildiz, O., Kuhlbrandt, W. Description: Cryo-EM structure of Polytomella F-ATP synthase, Rotary ...

New page

'''Unreleased structure'''

The entry 6rdk is ON HOLD

Authors: Murphy, B.J., Klusch, N., Yildiz, O., Kuhlbrandt, W.

Description: Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, composite map
[[Category: Unreleased Structures]]
[[Category: Yildiz, O]]
[[Category: Klusch, N]]
[[Category: Kuhlbrandt, W]]
[[Category: Murphy, B.J]]