› 7vy9

Electron Microscopy
2.9Å resolution

Membrane arm of active state CI from Q10-NADH dataset

Released:
DOI: 10.2210/pdb7vy9/pdb
PDB entry 7vy9 coloured by chain, front view.
PDB entry 7vy9 coloured by chain, side view.
PDB entry 7vy9 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-32197

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 29-mer (preferred)
PDBe Complex ID:
PDB-CPX-236725 (preferred)
Entry contents:
29 distinct polypeptide molecules
Macromolecules (29 distinct):
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 44 amino acids
Theoretical weight: 5.12 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S1A8 (Residues: 40-83; Coverage: 10%)
Gene name: NDUFS2
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: S
Molecule details ›
Chain: S
Length: 70 amino acids
Theoretical weight: 8.09 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GR43 (Residues: 1-70; Coverage: 100%)
Gene name: NDUFA1
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: U
Molecule details ›
Chain: U
Length: 83 amino acids
Theoretical weight: 9.09 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VQ42 (Residues: 2-84; Coverage: 99%)
Gene name: NDUFA3
Sequence domains: NADH dehydrogenase 1 alpha subcomplex subunit 3
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: V
Molecule details ›
Chain: V
Length: 140 amino acids
Theoretical weight: 14.56 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGM4 (Residues: 2-141; Coverage: 99%)
Gene name: NDUFA11
Sequence domains: Tim17/Tim22/Tim23/Pmp24 family
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: W
Molecule details ›
Chain: W
Length: 113 amino acids
Theoretical weight: 13.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1NRT6 (Residues: 32-144; Coverage: 79%)
Gene name: NDUFA13
Sequence domains: GRIM-19 protein
Acyl carrier protein Chain: X
Molecule details ›
Chain: X
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 beta subcomplex subunit 2, mitochondrial Chain: Y
Molecule details ›
Chain: Y
Length: 67 amino acids
Theoretical weight: 8.2 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A5G2QW32 (Residues: 52-118; Coverage: 56%)
Gene name: NDUFB2
Sequence domains: NADH dehydrogenase 1 beta subcomplex subunit 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: Z
Molecule details ›
Chain: Z
Length: 80 amino acids
Theoretical weight: 9.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VD84 (Residues: 12-91; Coverage: 82%)
Gene name: NDUFB3
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: a
Molecule details ›
Chain: a
Length: 138 amino acids
Theoretical weight: 16.28 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SGC6 (Residues: 52-189; Coverage: 73%)
Gene name: NDUFB5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: b
Molecule details ›
Chain: b
Length: 126 amino acids
Theoretical weight: 15.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480KM09 (Residues: 62-187; Coverage: 67%)
Gene name: NDUFB6
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 156 amino acids
Theoretical weight: 18.61 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RWL7 (Residues: 31-186; Coverage: 84%)
Gene name: NDUFB8
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: d
Molecule details ›
Chain: d
Length: 175 amino acids
Theoretical weight: 20.81 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LDC3 (Residues: 2-201; Coverage: 87%)
Gene name: NDUFB10
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Chain: e
Molecule details ›
Chain: e
Length: 104 amino acids
Theoretical weight: 12.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287BMW6 (Residues: 51-164; Coverage: 71%)
Gene name: NDUFB11
Sequence domains: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I)
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chain: f
Molecule details ›
Chain: f
Length: 49 amino acids
Theoretical weight: 5.88 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A1XQS6 (Residues: 28-76; Coverage: 65%)
Gene name: NDUFC1
Sequence domains: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: g
Molecule details ›
Chain: g
Length: 121 amino acids
Theoretical weight: 14.2 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480JRW3 (Residues: 2-122; Coverage: 99%)
Gene name: NDUFC2
Sequence domains: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: h
Molecule details ›
Chain: h
Length: 105 amino acids
Theoretical weight: 12.38 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SV23 (Residues: 2-106; Coverage: 99%)
Gene name: NDUFS5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH-ubiquinone oxidoreductase chain 2 Chain: i
Molecule details ›
Chain: i
Length: 347 amino acids
Theoretical weight: 39.08 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79875 (Residues: 1-347; Coverage: 100%)
Gene names: MT-ND2, MTND2, NADH2, ND2
Sequence domains:
NADH-ubiquinone oxidoreductase chain 3 Chain: j
Molecule details ›
Chain: j
Length: 115 amino acids
Theoretical weight: 13 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79880 (Residues: 1-115; Coverage: 100%)
Gene names: MT-ND3, MTND3, NADH3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-ubiquinone oxidoreductase chain 4L Chain: k
Molecule details ›
Chain: k
Length: 98 amino acids
Theoretical weight: 10.83 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P56632 (Residues: 1-98; Coverage: 100%)
Gene names: MT-ND4L, MTND4L, NADH4L, ND4L
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NADH-ubiquinone oxidoreductase chain 5 Chain: l
Molecule details ›
Chain: l
Length: 606 amino acids
Theoretical weight: 68.7 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q9TDR1 (Residues: 1-606; Coverage: 100%)
Gene names: MT-ND5, MTND5, NADH5, ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 6 Chain: m
Molecule details ›
Chain: m
Length: 175 amino acids
Theoretical weight: 19.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79882 (Residues: 1-175; Coverage: 100%)
Gene names: MT-ND6, MTND6, NADH6, ND6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 Chain: n
Molecule details ›
Chain: n
Length: 56 amino acids
Theoretical weight: 6.78 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D2CGH8 (Residues: 3-58; Coverage: 97%)
Gene name: NDUFB1
Sequence domains: MNLL subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: o
Molecule details ›
Chain: o
Length: 128 amino acids
Theoretical weight: 14.99 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1T6M0 (Residues: 2-129; Coverage: 99%)
Gene name: NDUFB4
Sequence domains: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: p
Molecule details ›
Chain: p
Length: 178 amino acids
Theoretical weight: 21.73 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GSE5 (Residues: 44-221; Coverage: 81%)
Gene name: NDUFB9
Sequence domains: Complex 1 protein (LYR family)
NADH-ubiquinone oxidoreductase chain 4 Chain: r
Molecule details ›
Chain: r
Length: 459 amino acids
Theoretical weight: 51.85 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79881 (Residues: 1-459; Coverage: 100%)
Gene names: MT-ND4, MTND4, NADH4, ND4
Sequence domains:
NADH-ubiquinone oxidoreductase chain 1 Chain: s
Molecule details ›
Chain: s
Length: 318 amino acids
Theoretical weight: 35.67 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79874 (Residues: 1-318; Coverage: 100%)
Gene names: MT-ND1, MTND1, NADH1, ND1
Sequence domains: NADH dehydrogenase
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: u
Molecule details ›
Chain: u
Length: 171 amino acids
Theoretical weight: 19.93 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SLR1 (Residues: 79-249; Coverage: 69%)
Gene name: NDUFA8
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 Chain: v
Molecule details ›
Chain: v
Length: 125 amino acids
Theoretical weight: 15.39 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SCH1 (Residues: 2-125; Coverage: 91%)
Gene name: NDUFB7
Sequence domains: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chain: w
Molecule details ›
Chain: w
Length: 320 amino acids
Theoretical weight: 36.79 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SIS9 (Residues: 38-357; Coverage: 90%)
Gene name: NDUFA10
Sequence domains: Deoxynucleoside kinase

Ligands and Environments

6 bound ligands:
Ligand PEE 9 x PEE
Ligand CDL 9 x CDL
Ligand 8Q1 1 x 8Q1
Ligand PLX 6 x PLX
Ligand UQ 1 x UQ
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-32197

Quick links

Citations

4 review citations

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