7VYI

Membrane arm of deactive state CI from Rotenone dataset

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

  • Deposited: 2021-11-14 Released: 2022-11-23 
  • 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: 3.10 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.K.Liu, T.Guo, R.Zhang, L.Yang, M.J.

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

  • DOI: 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, 7VYF, 7VYG, 7VYH, 7VYI

  • 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 ...

    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

    SUSTech Cryo-EM Facility Center, Southern University of Science & Technology, Shenzhen, China. maojunyang@tsinghua.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialA [auth Q]40Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A480JYS1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1B [auth S]70Sus scrofaMutation(s): 0 
Gene Names: NDUFA1
Membrane Entity: Yes 
UniProt
Find proteins for K7GR43 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3C [auth U]83Sus scrofaMutation(s): 0 
Gene Names: NDUFA3
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1VQ42 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11D [auth V]140Sus scrofaMutation(s): 0 
Gene Names: NDUFA11
Membrane Entity: Yes 
UniProt
Find proteins for I3LGM4 (Sus scrofa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13E [auth W]113Sus scrofaMutation(s): 0 
Gene Names: NDUFA13
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialF [auth X]88Sus scrofaMutation(s): 0 
Gene Names: NDUFAB1
UniProt
Find proteins for D0G781 (Sus scrofa)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialG [auth Y]70Sus scrofaMutation(s): 0 
Gene Names: NDUFB2
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1V766 (Sus scrofa)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3H [auth Z]84Sus scrofaMutation(s): 0 
Gene Names: NDUFB3
Membrane Entity: Yes 
UniProt
Find proteins for A0A287AS93 (Sus scrofa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialI [auth a]140Sus scrofaMutation(s): 0 
Gene Names: NDUFB5
Membrane Entity: Yes 
UniProt
Find proteins for F1SGC6 (Sus scrofa)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6J [auth b]126Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q2EN80 (Sus scrofa)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialK [auth c]156Sus scrofaMutation(s): 0 
Gene Names: NDUFB8
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10L [auth d]175Sus scrofaMutation(s): 0 
Gene Names: NDUFB10
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialM [auth e]107Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8D1EYI7 (Sus scrofa)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialN [auth f]42Sus scrofaMutation(s): 0 
Gene Names: NDUFC1
Membrane Entity: Yes 
UniProt
Find proteins for A1XQS6 (Sus scrofa)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2O [auth g]121Sus scrofaMutation(s): 0 
Gene Names: NDUFC2
Membrane Entity: Yes 
UniProt
Find proteins for A0A480JRW3 (Sus scrofa)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5P [auth h]105Sus scrofaMutation(s): 0 
Gene Names: NDUFS5
Membrane Entity: Yes 
UniProt
Find proteins for F1SV23 (Sus scrofa)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2Q [auth i]347Sus scrofaMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79875 (Sus scrofa)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3R [auth j]113Sus scrofaMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79880 (Sus scrofa)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LS [auth k]98Sus scrofaMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P56632 (Sus scrofa)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5T [auth l]603Sus scrofaMutation(s): 0 
Gene Names: NADH5ND5
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q71K68 (Sus scrofa)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6U [auth m]175Sus scrofaMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79882 (Sus scrofa)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1V [auth n]56Sus scrofaMutation(s): 0 
Gene Names: NDUFB1
Membrane Entity: Yes 
UniProt
Find proteins for F1SD73 (Sus scrofa)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4W [auth o]128Sus scrofaMutation(s): 0 
Gene Names: NDUFB4
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1T6M0 (Sus scrofa)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9X [auth p]178Sus scrofaMutation(s): 0 
Gene Names: NDUFB9
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1T0A8 (Sus scrofa)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4Y [auth r]459Sus scrofaMutation(s): 0 
Gene Names: NADH4
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q7IIB7 (Sus scrofa)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1Z [auth s]318Sus scrofaMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for O79874 (Sus scrofa)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8AA [auth u]171Sus scrofaMutation(s): 0 
Gene Names: NDUFA8
UniProt
Find proteins for F1SLR1 (Sus scrofa)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7BA [auth v]125Sus scrofaMutation(s): 1 
Gene Names: NDUFB7
Membrane Entity: Yes 
UniProt
Find proteins for F1SCH1 (Sus scrofa)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialCA [auth w]320Sus scrofaMutation(s): 0 
Gene Names: NDUFA10
UniProt
Find proteins for F1SIS9 (Sus scrofa)
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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GA [auth a],
KA [auth g],
LA [auth i],
OA [auth l],
UA [auth r],
GA [auth a],
KA [auth g],
LA [auth i],
OA [auth l],
UA [auth r],
VA [auth r]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
UQ (Subject of Investigation/LOI)
Query on UQ

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

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HA [auth a],
JA [auth g],
NA [auth j],
SA [auth r],
TA [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
 Ligand Interaction
PEE (Subject of Investigation/LOI)
Query on PEE

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DA [auth U],
EA [auth U],
IA [auth b],
MA [auth i],
PA [auth l],
DA [auth U],
EA [auth U],
IA [auth b],
MA [auth i],
PA [auth l],
QA [auth m],
RA [auth r]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

Download Ideal Coordinates CCD File 
FA [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
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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: 2022-11-23
    Type: Initial release