7VBN

Matrix arm of deactive state CI from DQ-NADH dataset

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 2021-08-31 Released: 2022-04-06 
  • 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: 2.40 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial431Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A4X1SZP7 (Sus scrofa)
Explore A0A4X1SZP7 
Go to UniProtKB:  A0A4X1SZP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1SZP7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial176Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BDC0 (Sus scrofa)
Explore A0A287BDC0 
Go to UniProtKB:  A0A287BDC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287BDC0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial156Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1TL60 (Sus scrofa)
Explore A0A8D1TL60 
Go to UniProtKB:  A0A8D1TL60
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D1TL60
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6D [auth E]115Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SJP6 (Sus scrofa)
Explore F1SJP6 
Go to UniProtKB:  F1SJP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1SJP6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2E [auth F]86Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RGE3 (Sus scrofa)
Explore F1RGE3 
Go to UniProtKB:  F1RGE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1RGE3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialF [auth G]88Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AAR5 (Sus scrofa)
Explore A0A287AAR5 
Go to UniProtKB:  A0A287AAR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287AAR5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5G [auth H]112Sus scrofaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7H [auth I]112Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VLA2 (Sus scrofa)
Explore A0A4X1VLA2 
Go to UniProtKB:  A0A4X1VLA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1VLA2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase ubiquinone 1 alpha subcomplex subunit 9, mitochondrialI [auth J]341Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AE88 (Sus scrofa)
Explore A0A287AE88 
Go to UniProtKB:  A0A287AE88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287AE88
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialJ [auth K]42Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LRR4 (Sus scrofa)
Explore I3LRR4 
Go to UniProtKB:  I3LRR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LRR4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialK [auth L]125Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1SN37 (Sus scrofa)
Explore A0A4X1SN37 
Go to UniProtKB:  A0A4X1SN37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1SN37
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialL [auth M]690Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1V1H9 (Sus scrofa)
Explore A0A4X1V1H9 
Go to UniProtKB:  A0A4X1V1H9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1V1H9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12M [auth N]144Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SQP4 (Sus scrofa)
Explore F1SQP4 
Go to UniProtKB:  F1SQP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1SQP4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialN [auth O]217Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BG40 (Sus scrofa)
Explore A0A287BG40 
Go to UniProtKB:  A0A287BG40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287BG40
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialO [auth P]208Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZNN4 (Sus scrofa)
Explore A0A286ZNN4 
Go to UniProtKB:  A0A286ZNN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A286ZNN4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialP [auth Q]385Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S1A8 (Sus scrofa)
Explore F1S1A8 
Go to UniProtKB:  F1S1A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1S1A8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialQ [auth T]96Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S031 (Sus scrofa)
Explore F1S031 
Go to UniProtKB:  F1S031
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1S031
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13R [auth W]29Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1NRT6 (Sus scrofa)
Explore A0A8D1NRT6 
Go to UniProtKB:  A0A8D1NRT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D1NRT6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
GA [auth N]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PLX (Subject of Investigation/LOI)
Query on PLX

Download Ideal Coordinates CCD File 
Z [auth C](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
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
BA [auth J]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PEE (Subject of Investigation/LOI)
Query on PEE

Download Ideal Coordinates CCD File 
Y [auth C]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
U [auth A]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

Download Ideal Coordinates CCD File 
AA [auth G]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
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
T [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
CA [auth M]
DA [auth M]
S [auth A]
V [auth B]
W [auth B]
CA [auth M],
DA [auth M],
S [auth A],
V [auth B],
W [auth B],
X [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
EA [auth M],
HA [auth O]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
IA [auth T]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
FA [auth M]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
P [auth Q]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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, 32030056, 21532004, 31570733, 31800620

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release