7w4e - Revision history

OCA at 14:52, 13 August 2026

2026-08-13T14:52:17Z

← Older revision		Revision as of 14:52, 13 August 2026
Line 3:		Line 3:
	<StructureSection load='7w4e' size='340' side='right'caption='[[7w4e]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='7w4e' size='340' side='right'caption='[[7w4e]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7w4e]] is a 11 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=7W4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[7w4e]] 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=7W4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W4E 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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=PLX:(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL'>PLX~~</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=UQ1:UBIQUINONE-1'>UQ1</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]] 3Å</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-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl]+dodecanethioate'>8Q1</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=PLX:(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL'>PLX</scene>, <scene name='pdbligand=UQ:COENZYME+Q10,+(2Z,6E,10Z,14E,18E,22E,26Z)-ISOMER'>UQ</scene>, <scene name='pdbligand=UQ1:UBIQUINONE-1'>UQ1</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=7w4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w4e OCA], [https://pdbe.org/7w4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w4e RCSB], [https://www.ebi.ac.uk/pdbsum/7w4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w4e 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=7w4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w4e OCA], [https://pdbe.org/7w4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w4e RCSB], [https://www.ebi.ac.uk/pdbsum/7w4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/~~A0A480VKQ8_PIG A0A480VKQ8_PIG~~] ~~Accessory~~ subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I)~~, that is believed to be not involved in catalysis. Complex I functions in the~~ transfer ~~of electrons~~ from NADH to the respiratory chain~~. The immediate electron acceptor for the enzyme is believed to be~~ ubiquinone~~.[PIRNR:PIRNR006643]~~		[https://www.uniprot.org/uniprot/A0A8D1TL60_PIG A0A8D1TL60_PIG] Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Essential for the catalytic activity of complex I.[ARBA:ARBA00024297]
	~~<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.~~

	~~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>~~

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7w4e" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:17, 1 February 2023

2023-02-01T11:17:10Z

← Older revision		Revision as of 11:17, 1 February 2023
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	The ~~entry 7w4e~~ is ~~ON HOLD~~		==Active state CI from Q1-NADH dataset, Subclass 3==
			<StructureSection load='7w4e' size='340' side='right'caption='[[7w4e]], [[Resolution\|resolution]] 3.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[7w4e]] is a 11 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=7W4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W4E 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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=PLX:(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL'>PLX</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=UQ1:UBIQUINONE-1'>UQ1</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=7w4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w4e OCA], [https://pdbe.org/7w4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w4e RCSB], [https://www.ebi.ac.uk/pdbsum/7w4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w4e ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/A0A480VKQ8_PIG A0A480VKQ8_PIG] Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed to be not involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone.[PIRNR:PIRNR006643]
			<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~~: ~~Active state CI from Q1-NADH dataset, Subclass 3~~		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 7w4e" 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 "7w4e" [edit=sysop:move=sysop]

2021-12-08T08:43:49Z

Protected "7w4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:43, 8 December 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7w4e is ON HOLD Authors: Gu, J.K., Yang, M.J. Description: Active state CI from Q1-NADH dataset, Subclass 3 Category: Unreleased Structures [[C...

2021-12-08T08:43:48Z

New page: '''Unreleased structure''' The entry 7w4e is ON HOLD Authors: Gu, J.K., Yang, M.J. Description: Active state CI from Q1-NADH dataset, Subclass 3 Category: Unreleased Structures [[C...

New page

'''Unreleased structure'''

The entry 7w4e is ON HOLD

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

Description: Active state CI from Q1-NADH dataset, Subclass 3
[[Category: Unreleased Structures]]
[[Category: Gu, J.K]]
[[Category: Yang, M.J]]