[English] 日本語

Yorodumi Papers

- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

-
Structure paper

Title	The coupling mechanism of mammalian mitochondrial complex I.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 29, Issue 2, Page 172-182, Year 2022
Publish date	Feb 10, 2022
Authors	Jinke Gu / Tianya Liu / Runyu Guo / Laixing Zhang / Maojun Yang /
PubMed Abstract	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 ...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 Å, 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.
External links	Nat Struct Mol Biol / PubMed:35145322
Methods	EM (single particle)
Resolution	2.4 - 3.5 Å
Structure data	31640 7v2c EMDB-31640, PDB-7v2c: Active state complex I from Q10 dataset Method: EM (single particle) / Resolution: 2.9 Å 31641 7v2d EMDB-31641, PDB-7v2d: Deactive state complex I from Q10 dataset Method: EM (single particle) / Resolution: 3.3 Å 31643 7v2e EMDB-31643, PDB-7v2e: Active state complex I from Q10-NADH dataset Method: EM (single particle) / Resolution: 2.8 Å 31644 7v2f EMDB-31644, PDB-7v2f: Deactive state complex I from Q10-NADH dataset Method: EM (single particle) / Resolution: 3.1 Å 31645 7v2h EMDB-31645, PDB-7v2h: Active state complex I from DQ-NADH dataset Method: EM (single particle) / Resolution: 2.5 Å 31646 7v2k EMDB-31646, PDB-7v2k: Deactive state complex I from DQ-NADH dataset Method: EM (single particle) / Resolution: 2.7 Å 31647 7v2r EMDB-31647, PDB-7v2r: Active state complex I from Q1-NADH dataset Method: EM (single particle) / Resolution: 2.6 Å 31648 7v30 EMDB-31648, PDB-7v30: Deactive state complex I from Q1-NADH dataset Method: EM (single particle) / Resolution: 2.7 Å 31649 7v31 EMDB-31649, PDB-7v31: Active state complex I from rotenone dataset Method: EM (single particle) / Resolution: 2.9 Å 31650 7v32 EMDB-31650, PDB-7v32: Deactive state complex I from rotenone dataset Method: EM (single particle) / Resolution: 2.9 Å 31651 7v33 EMDB-31651, PDB-7v33: Active state complex I from rotenone-NADH dataset Method: EM (single particle) / Resolution: 2.5 Å 31652 7v3m EMDB-31652, PDB-7v3m: Deactive state complex I from rotenone-NADH dataset Method: EM (single particle) / Resolution: 2.8 Å 31874 7vb7 EMDB-31874, PDB-7vb7: Matrix arm of active state CI from DQ-NADH dataset Method: EM (single particle) / Resolution: 2.4 Å 31881 7vbl EMDB-31881, PDB-7vbl: Membrane arm of active state CI from DQ-NADH dataset Method: EM (single particle) / Resolution: 2.6 Å 31883 7vbn EMDB-31883, PDB-7vbn: Matrix arm of deactive state CI from DQ-NADH dataset Method: EM (single particle) / Resolution: 2.4 Å 31884 7vbp EMDB-31884, PDB-7vbp: Membrane arm of deactive state CI from DQ-NADH dataset Method: EM (single particle) / Resolution: 2.8 Å 31886 7vbz EMDB-31886, PDB-7vbz: Matrix arm of active state CI from Rotenone-NADH dataset Method: EM (single particle) / Resolution: 2.4 Å 31887 7vc0 EMDB-31887, PDB-7vc0: Membrane arm of active state CI from Rotenone-NADH dataset Method: EM (single particle) / Resolution: 2.6 Å 32154 7vwj EMDB-32154, PDB-7vwj: Matrix arm of deactive state CI from rotenone-NADH dataset Method: EM (single particle) / Resolution: 2.6 Å 32155 7vwl EMDB-32155, PDB-7vwl: Membrane arm of deactive state CI from rotenone-NADH dataset Method: EM (single particle) / Resolution: 2.7 Å 32186 7vxp EMDB-32186, PDB-7vxp: Matrix arm of active state CI from Q10 dataset Method: EM (single particle) / Resolution: 2.7 Å 32187 7vxs EMDB-32187, PDB-7vxs: Membrane arm of active state CI from Q10 dataset Method: EM (single particle) / Resolution: 2.9 Å 32188 7vxu EMDB-32188, PDB-7vxu: Matrix arm of deactive state CI from Q10 dataset Method: EM (single particle) / Resolution: 2.8 Å 32191 7vy1 EMDB-32191, PDB-7vy1: Membrane arm of deactive state CI from Q10 dataset Method: EM (single particle) / Resolution: 3.3 Å 32196 7vy8 EMDB-32196, PDB-7vy8: Matrix arm of active state CI from Q10-NADH dataset Method: EM (single particle) / Resolution: 2.6 Å 32197 7vy9 EMDB-32197, PDB-7vy9: Membrane arm of active state CI from Q10-NADH dataset Method: EM (single particle) / Resolution: 2.9 Å 32198 7vya EMDB-32198, PDB-7vya: Matrix arm of deactive state CI from Q10-NADH dataset Method: EM (single particle) / Resolution: 2.8 Å 32202 7vye EMDB-32202, PDB-7vye: Membrane arm of deactive state CI from Q10-NADH dataset Method: EM (single particle) / Resolution: 3.1 Å 32203 7vyf EMDB-32203, PDB-7vyf: Matrix arm of active state CI from Rotenone dataset Method: EM (single particle) / Resolution: 2.8 Å 32204 7vyg EMDB-32204, PDB-7vyg: Membrane arm of active state CI from rotenone dataset Method: EM (single particle) / Resolution: 2.9 Å 32205 7vyh EMDB-32205, PDB-7vyh: Matrix arm of deactive state CI from Rotenone dataset Method: EM (single particle) / Resolution: 2.9 Å 32206 7vyi EMDB-32206, PDB-7vyi: Membrane arm of deactive state CI from Rotenone dataset Method: EM (single particle) / Resolution: 3.1 Å 32210 7vyn EMDB-32210, PDB-7vyn: Matrix arm of active state CI from Q1-NADH dataset Method: EM (single particle) / Resolution: 2.4 Å 32214 7vys EMDB-32214, PDB-7vys: Membrane arm of active state CI from Q1-NADH dataset Method: EM (single particle) / Resolution: 2.5 Å 32218 7vz1 EMDB-32218, PDB-7vz1: Matrix arm of deactive state CI from Q1-NADH dataset Method: EM (single particle) / Resolution: 2.5 Å 32222 7vz8 EMDB-32222, PDB-7vz8: Membrane arm of deactive state CI from Q1-NADH dataset Method: EM (single particle) / Resolution: 2.7 Å 32230 7vzv EMDB-32230, PDB-7vzv: Active state CI from Q10 dataset, Subclass 1 Method: EM (single particle) / Resolution: 3.2 Å 32231 7vzw EMDB-32231, PDB-7vzw: Active state CI from Q10 dataset, Subclass 2 Method: EM (single particle) / Resolution: 3.2 Å 32232 7w00 EMDB-32232, PDB-7w00: Deactive state CI from Q10 dataset, Subclass 1 Method: EM (single particle) / Resolution: 3.5 Å 32242 7w0h EMDB-32242, PDB-7w0h: Deactive state CI from Q10 dataset, Subclass 2 Method: EM (single particle) / Resolution: 3.4 Å 32248 7w0r EMDB-32248, PDB-7w0r: Active state CI from Q10-NADH dataset, Subclass 1 Method: EM (single particle) / Resolution: 2.8 Å 32249 7w0y EMDB-32249, PDB-7w0y: Active state CI from Q10-NADH dataset, Subclass 2 Method: EM (single particle) / Resolution: 3.4 Å 32253 7w1o EMDB-32253, PDB-7w1o: Deactive state CI from Q10-NADH dataset, Subclass 1 Method: EM (single particle) / Resolution: 3.5 Å 32254 7w1p EMDB-32254, PDB-7w1p: Deactive state CI from Q10-NADH dataset, Subclass 2 Method: EM (single particle) / Resolution: 3.1 Å 32255 7w1t EMDB-32255, PDB-7w1t: Active state CI from Rotenone dataset, Subclass 1 Method: EM (single particle) / Resolution: 3.0 Å 32256 7w1u EMDB-32256, PDB-7w1u: Active state CI from Rotenone dataset, Subclass 2 Method: EM (single particle) / Resolution: 3.2 Å 32257 7w1v EMDB-32257, PDB-7w1v: Active state CI from Rotenone-NADH dataset, Subclass 1 Method: EM (single particle) / Resolution: 3.0 Å 32259 7w1z EMDB-32259, PDB-7w1z: Active state CI from Rotenone-NADH dataset, Subclass 2 Method: EM (single particle) / Resolution: 2.6 Å 32260 7w20 EMDB-32260, PDB-7w20: Active state CI from Rotenone-NADH dataset, Subclass 3 Method: EM (single particle) / Resolution: 3.0 Å 32263 7w2k EMDB-32263, PDB-7w2k: Deactive state CI from Rotenone-NADH dataset, Subclass 1 Method: EM (single particle) / Resolution: 2.9 Å 32264 7w2l EMDB-32264, PDB-7w2l: Deactive state CI from Rotenone-NADH dataset, Subclass 2 Method: EM (single particle) / Resolution: 3.0 Å 32265 7w2r EMDB-32265, PDB-7w2r: Active state CI from DQ-NADH dataset, Subclass 1 Method: EM (single particle) / Resolution: 2.9 Å 32266 7w2u EMDB-32266, PDB-7w2u: Active state CI from DQ-NADH dataset, Subclass 2 Method: EM (single particle) / Resolution: 2.6 Å 32267 7w2y EMDB-32267, PDB-7w2y: Active state CI from DQ-NADH dataset, Subclass 3 Method: EM (single particle) / Resolution: 2.7 Å 32269 7w31 EMDB-32269, PDB-7w31: Deactive state CI from DQ-NADH dataset, Subclass 1 Method: EM (single particle) / Resolution: 3.1 Å 32270 7w32 EMDB-32270, PDB-7w32: Deactive state CI from DQ-NADH dataset, Subclass 2 Method: EM (single particle) / Resolution: 2.9 Å 32271 7w35 EMDB-32271, PDB-7w35: Deactive state CI from DQ-NADH dataset, Subclass 3 Method: EM (single particle) / Resolution: 3.0 Å 32300 7w4c EMDB-32300, PDB-7w4c: Active state CI from Q1-NADH dataset, Subclass 1 Method: EM (single particle) / Resolution: 2.7 Å 32301 7w4d EMDB-32301, PDB-7w4d: Active state CI from Q1-NADH dataset, Subclass 2 Method: EM (single particle) / Resolution: 3.0 Å 32302 7w4e EMDB-32302, PDB-7w4e: Active state CI from Q1-NADH dataset, Subclass 3 Method: EM (single particle) / Resolution: 3.0 Å 32303 7w4f EMDB-32303, PDB-7w4f: Active state CI from Q1-NADH dataset, Subclass 4 Method: EM (single particle) / Resolution: 2.7 Å 32304 7w4g EMDB-32304, PDB-7w4g: Active state CI from Q1-NADH dataset, Subclass 5 Method: EM (single particle) / Resolution: 3.1 Å 32305 7w4j EMDB-32305, PDB-7w4j: Deactive state CI from Q1-NADH dataset, Subclass 1 Method: EM (single particle) / Resolution: 3.2 Å 32306 7w4k EMDB-32306, PDB-7w4k: Deactive state CI from Q1-NADH dataset, Subclass 2 Method: EM (single particle) / Resolution: 3.2 Å 32307 7w4l EMDB-32307, PDB-7w4l: Deactive state CI from Q1-NADH dataset, Subclass 3 Method: EM (single particle) / Resolution: 3.1 Å 32308 7w4m EMDB-32308, PDB-7w4m: Deactive state CI from Q1-NADH dataset, Subclass 4 Method: EM (single particle) / Resolution: 3.3 Å 32309 7w4n EMDB-32309, PDB-7w4n: Deactive state CI from Q1-NADH dataset, Subclass 5 Method: EM (single particle) / Resolution: 3.0 Å 32312 7w4q EMDB-32312, PDB-7w4q: Deactive state CI from Q1-NADH dataset, Subclass 6 Method: EM (single particle) / Resolution: 3.3 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER / Iron–sulfur cluster ChemComp-FMN: FLAVIN MONONUCLEOTIDE / Flavin mononucleotide ChemComp-PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipidYM / Discrete optimized protein energy ChemComp-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 / phospholipidYM ChemComp-8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate ChemComp-NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate ChemComp-UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer ChemComp-CDL: CARDIOLIPIN / phospholipidYM / Cardiolipin ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide ChemComp-DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione ChemComp-UQ1: UBIQUINONE-1 ChemComp-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 / Rotenone ChemComp-HOH: WATER / Water ChemComp-TYR: TYROSINE / Tyrosine
Source	sus scrofa (pig) pig (pig)
Keywords	ELECTRON TRANSPORT / Respiratory / Complex / mammalian / complex I / mitochondrial / ELECTRON T

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

Database of articles cited by EMDB, PDB, and SASBDB entries
Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi