› 7vyh

Electron Microscopy
2.9Å resolution

Matrix arm of deactive state CI from Rotenone dataset

Released:
DOI: 10.2210/pdb7vyh/pdb
PDB entry 7vyh coloured by chain, front view.
PDB entry 7vyh coloured by chain, side view.
PDB entry 7vyh coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
The coupling mechanism of mammalian mitochondrial complex I.
Gu J, Liu T, Guo R, Zhang L, Yang M
Nat Struct Mol Biol 29 172-182 (2022)
PMID: 35145322
Related structures: EMD-32205

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-236685 (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 431 amino acids
Theoretical weight: 47.27 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1SZP7 (Residues: 28-458; Coverage: 93%)
Gene name: NDUFV1
Sequence domains:
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 176 amino acids
Theoretical weight: 20.21 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BDC0 (Residues: 37-212; Coverage: 83%)
Gene name: NDUFS8
Sequence domains: 4Fe-4S dicluster domain
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 156 amino acids
Theoretical weight: 17.87 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1TL60 (Residues: 41-196; Coverage: 80%)
Gene name: NDUFS7
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: E
Molecule details ›
Chain: E
Length: 115 amino acids
Theoretical weight: 13.81 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SJP6 (Residues: 40-154; Coverage: 75%)
Gene name: NDUFA6
Sequence domains: Complex 1 protein (LYR family)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: F
Molecule details ›
Chain: F
Length: 86 amino acids
Theoretical weight: 9.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RGE3 (Residues: 14-99; Coverage: 87%)
Gene name: NDUFA2
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Acyl carrier protein Chain: G
Molecule details ›
Chain: G
Length: 88 amino acids
Theoretical weight: 10.13 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AAR5 (Residues: 69-156; Coverage: 56%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: H
Molecule details ›
Chain: H
Length: 112 amino acids
Theoretical weight: 12.95 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BAW0 (Residues: 5-116; Coverage: 97%)
Gene name: NDUFA5
Sequence domains: ETC complex I subunit conserved region
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 Chain: I
Molecule details ›
Chain: I
Length: 112 amino acids
Theoretical weight: 12.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8W4F7N8 (Residues: 2-113; Coverage: 99%)
Gene name: NDUFA7
Sequence domains: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: J
Molecule details ›
Chain: J
Length: 341 amino acids
Theoretical weight: 38.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AE88 (Residues: 36-406; Coverage: 84%)
Gene name: NDUFA9
Sequence domains: NAD dependent epimerase/dehydratase family
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial Chain: K
Molecule details ›
Chain: K
Length: 42 amino acids
Theoretical weight: 5.05 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LRR4 (Residues: 69-110; Coverage: 38%)
Gene name: NDUFV3
Sequence domains: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Chain: L
Molecule details ›
Chain: L
Length: 125 amino acids
Theoretical weight: 14.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: G8IFA6 (Residues: 51-175; Coverage: 71%)
Sequence domains: NADH dehydrogenase ubiquinone Fe-S protein 4
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial Chain: M
Molecule details ›
Chain: M
Length: 690 amino acids
Theoretical weight: 75.77 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1V1H9 (Residues: 29-718; Coverage: 95%)
Gene name: NDUFS1
Sequence domains:
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Chain: N
Molecule details ›
Chain: N
Length: 144 amino acids
Theoretical weight: 17.03 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SQP4 (Residues: 2-145; Coverage: 99%)
Gene name: NDUFA12
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: O
Molecule details ›
Chain: O
Length: 217 amino acids
Theoretical weight: 23.83 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BG40 (Residues: 33-249; Coverage: 87%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial Chain: P
Molecule details ›
Chain: P
Length: 208 amino acids
Theoretical weight: 24.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZNN4 (Residues: 43-250; Coverage: 79%)
Gene name: NDUFS3
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 385 amino acids
Theoretical weight: 44.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S1A8 (Residues: 85-469; Coverage: 86%)
Gene name: NDUFS2
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 96 amino acids
Theoretical weight: 10.57 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S031 (Residues: 28-123; Coverage: 78%)
Gene name: NDUFS6
Sequence domains: Zinc-finger domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: W
Molecule details ›
Chain: W
Length: 29 amino acids
Theoretical weight: 3.2 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1NRT6 (Residues: 3-31; Coverage: 20%)
Gene name: NDUFA13

Ligands and Environments

10 bound ligands:
Ligand SF4 6 x SF4
Ligand FMN 1 x FMN
Ligand PEE 1 x PEE
Ligand PLX 1 x PLX
Ligand 8Q1 1 x 8Q1
Ligand NDP 1 x NDP
Ligand FES 2 x FES
Ligand MG 1 x MG
Ligand CDL 1 x CDL
Ligand ZN 1 x ZN
1 modified residue:
Ligand 2MR 1 x 2MR

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-32205

Quick links

Citations

4 review citations

Structure of respiratory complex I - An emerging blueprint for the mechanism.
Kampjut et al. (2022)
3 more