7vyf - Revision history

OCA at 21:23, 28 June 2023

OCA — Wed, 28 Jun 2023 21:23:53 GMT

←Older revision		Revision as of 21:23, 28 June 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7vyf]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VYF FirstGlance]. <br>		<table><tr><td colspan='2'>[[7vyf]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VYF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=8Q1:S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=970:(2R,6aS,12aS)-8,9-dimethoxy-2-(prop-1-en-2-yl)-1,2,12,12a-tetrahydrofuro[2,3 7,8][1]benzopyrano[2,3-c][1]benzopyran-6(6aH)-one'>970</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UQ:COENZYME+Q10,+(2Z,6E,10Z,14E,18E,22E,26Z)-ISOMER'>UQ</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]] 2.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=8Q1:S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=970:(2R,6aS,12aS)-8,9-dimethoxy-2-(prop-1-en-2-yl)-1,2,12,12a-tetrahydrofuro[2,3 7,8][1]benzopyrano[2,3-c][1]benzopyran-6(6aH)-one'>970</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UQ:COENZYME+Q10,+(2Z,6E,10Z,14E,18E,22E,26Z)-ISOMER'>UQ</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'>[https://proteopedia.org/fgij/fg.htm?mol=7vyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vyf OCA], [https://pdbe.org/7vyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vyf RCSB], [https://www.ebi.ac.uk/pdbsum/7vyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vyf 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=7vyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vyf OCA], [https://pdbe.org/7vyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vyf RCSB], [https://www.ebi.ac.uk/pdbsum/7vyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vyf ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:07, 24 November 2022

OCA — Thu, 24 Nov 2022 10:07:42 GMT

←Older revision		Revision as of 10:07, 24 November 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7vyf is ~~ON HOLD~~	+	==Matrix arm of active state CI from Rotenone dataset==
		+	<StructureSection load='7vyf' size='340' side='right'caption='[[7vyf]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7vyf]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VYF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=8Q1:S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=970:(2R,6aS,12aS)-8,9-dimethoxy-2-(prop-1-en-2-yl)-1,2,12,12a-tetrahydrofuro[2,3 7,8][1]benzopyrano[2,3-c][1]benzopyran-6(6aH)-one'>970</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UQ:COENZYME+Q10,+(2Z,6E,10Z,14E,18E,22E,26Z)-ISOMER'>UQ</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'>[https://proteopedia.org/fgij/fg.htm?mol=7vyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vyf OCA], [https://pdbe.org/7vyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vyf RCSB], [https://www.ebi.ac.uk/pdbsum/7vyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vyf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F1RVN1_PIG F1RVN1_PIG]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 A, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI.

-	~~Authors: Gu~~, J~~.K.~~, ~~Yang~~, M.J.	+	The coupling mechanism of mammalian mitochondrial complex I.,Gu J, Liu T, Guo R, Zhang L, Yang M Nat Struct Mol Biol. 2022 Feb;29(2):172-182. doi: 10.1038/s41594-022-00722-w. , Epub 2022 Feb 10. PMID:35145322<ref>PMID:35145322</ref>

-	~~Description: Matrix arm~~ of ~~active state CI from Rotenone dataset~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Gu~~, J.K~~]]	+	<div class="pdbe-citations 7vyf" style="background-color:#fffaf0;"></div>
-	[[Category: Yang~~, M.J~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sus scrofa]]
		+	[[Category: Gu JK]]
		+	[[Category: Yang MJ]]

OCA: Protected "7vyf" [edit=sysop:move=sysop]

OCA — Wed, 24 Nov 2021 11:06:33 GMT

Protected "7vyf" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:06, 24 November 2021

OCA: New page: '''Unreleased structure''' The entry 7vyf is ON HOLD Authors: Gu, J.K., Yang, M.J. Description: Matrix arm of active state CI from Rotenone dataset Category: Unreleased Structures ...

OCA — Wed, 24 Nov 2021 11:06:32 GMT

New page: '''Unreleased structure''' The entry 7vyf is ON HOLD Authors: Gu, J.K., Yang, M.J. Description: Matrix arm of active state CI from Rotenone dataset Category: Unreleased Structures ...

New page

'''Unreleased structure'''

The entry 7vyf is ON HOLD

Authors: Gu, J.K., Yang, M.J.

Description: Matrix arm of active state CI from Rotenone dataset
[[Category: Unreleased Structures]]
[[Category: Gu, J.K]]
[[Category: Yang, M.J]]