7VY9

Membrane arm of active state CI from Q10-NADH dataset

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Sus scrofa
  • Mutation(s): Yes 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2021-11-13 Released: 2022-12-14 
  • Deposition Author(s): Gu, J.K., Yang, M.J.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The coupling mechanism of mammalian mitochondrial complex I.

Gu, J.Liu, T.Guo, R.Zhang, L.Yang, M.

(2022) Nat Struct Mol Biol 29: 172-182

  • DOI: https://doi.org/10.1038/s41594-022-00722-w
  • Primary Citation of Related Structures:  
    7V2C, 7V2D, 7V2E, 7V2F, 7V2H, 7V2K, 7V2R, 7V30, 7V31, 7V32, 7V33, 7V3M, 7VB7, 7VBL, 7VBN, 7VBP, 7VBZ, 7VC0, 7VWJ, 7VWL, 7VXP, 7VXS, 7VXU, 7VY1, 7VY8, 7VY9, 7VYA, 7VYE, 7VYF, 7VYG, 7VYH, 7VYI, 7VYN, 7VYS, 7VZ1, 7VZ8, 7VZV, 7VZW, 7W00, 7W0H, 7W0R, 7W0Y, 7W1O, 7W1P, 7W1T, 7W1U, 7W1V, 7W1Z, 7W20, 7W2K

  • 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 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.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialA [auth Q]44Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1S1A8 (Sus scrofa)
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UniProt GroupF1S1A8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1B [auth S]70Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K7GR43 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3C [auth U]83Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1VQ42 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11D [auth V]140Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I3LGM4 (Sus scrofa)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13E [auth W]113Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8D1NRT6 (Sus scrofa)
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UniProt GroupA0A8D1NRT6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinF [auth X]88Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AAR5 (Sus scrofa)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialG [auth Y]67Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A5G2QW32 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3H [auth Z]80Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1VD84 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialI [auth a]138Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1SGC6 (Sus scrofa)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6J [auth b]126Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A480KM09 (Sus scrofa)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialK [auth c]156Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1RWL7 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10L [auth d]175Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialM [auth e]104Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialN [auth f]49Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1XQS6 (Sus scrofa)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2O [auth g]121Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A480JRW3 (Sus scrofa)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5P [auth h]105Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1SV23 (Sus scrofa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2Q [auth i]347Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79875 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3R [auth j]115Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79880 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LS [auth k]98Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P56632 (Sus scrofa)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5T [auth l]606Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9TDR1 (Sus scrofa)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6U [auth m]175Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79882 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1V [auth n]56Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8D2CGH8 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4W [auth o]128Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1T6M0 (Sus scrofa)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9X [auth p]178Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for K7GSE5 (Sus scrofa)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4Y [auth r]459Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79881 (Sus scrofa)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1Z [auth s]318Sus scrofaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79874 (Sus scrofa)
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UniProt GroupO79874
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8AA [auth u]171Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SLR1 (Sus scrofa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7BA [auth v]125Sus scrofaMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for F1SCH1 (Sus scrofa)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialCA [auth w]320Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SIS9 (Sus scrofa)
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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AB [auth s]
EA [auth V]
FA [auth V]
IA [auth a]
LA [auth g]
AB [auth s],
EA [auth V],
FA [auth V],
IA [auth a],
LA [auth g],
PA [auth k],
RA [auth l],
SA [auth l],
VA [auth n]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
UQ (Subject of Investigation/LOI)
Query on UQ

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CB [auth s]Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
PLX (Subject of Investigation/LOI)
Query on PLX

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JA [auth a]
KA [auth g]
NA [auth j]
OA [auth j]
XA [auth r]
JA [auth a],
KA [auth g],
NA [auth j],
OA [auth j],
XA [auth r],
YA [auth r]
(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
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
PEE (Subject of Investigation/LOI)
Query on PEE

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BB [auth s]
DA [auth Q]
GA [auth W]
MA [auth j]
QA [auth l]
BB [auth s],
DA [auth Q],
GA [auth W],
MA [auth j],
QA [auth l],
TA [auth l],
UA [auth l],
WA [auth r],
ZA [auth s]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

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HA [auth X]S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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DB [auth w]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0504600 and 2016YFA0501100
National Natural Science Foundation of China (NSFC)China31625008
National Natural Science Foundation of China (NSFC)China32030056, 21532004 and 31570733 and 31800620

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release