› 5z62

Electron Microscopy
3.6Å resolution

Structure of human cytochrome c oxidase

Released:
DOI: 10.2210/pdb5z62/pdb
PDB entry 5z62 coloured by chain, front view.
PDB entry 5z62 coloured by chain, side view.
PDB entry 5z62 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the intact 14-subunit human cytochrome c oxidase.
Zong S, Wu M, Gu J, Liu T, Guo R, Yang M
Cell Res 28 1026-1034 (2018)
PMID: 30030519
Related structures: EMD-6896

Function and Biology Details

Reaction catalysed: 
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126316 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Cytochrome c oxidase subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 513 amino acids
Theoretical weight: 57.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00395 (Residues: 1-513; Coverage: 100%)
Gene names: COI, COXI, MT-CO1, MTCO1
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Cytochrome c oxidase subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 227 amino acids
Theoretical weight: 25.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00403 (Residues: 1-227; Coverage: 100%)
Gene names: COII, COX2, COXII, MT-CO2, MTCO2
Sequence domains:
Structure domains:
Cytochrome c oxidase subunit 3 Chain: C
Molecule details ›
Chain: C
Length: 260 amino acids
Theoretical weight: 29.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00414 (Residues: 2-261; Coverage: 100%)
Gene names: COIII, COXIII, MT-CO3, MTCO3
Sequence domains: Cytochrome c oxidase subunit III
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 144 amino acids
Theoretical weight: 16.89 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P13073 (Residues: 26-169; Coverage: 85%)
Gene names: COX4, COX4I1
Sequence domains: Cytochrome c oxidase subunit IV
Structure domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 5A, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 109 amino acids
Theoretical weight: 12.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P20674 (Residues: 42-150; Coverage: 73%)
Gene name: COX5A
Sequence domains: Cytochrome c oxidase subunit Va
Structure domains: Cytochrome c oxidase, subunit Va/VI
Cytochrome c oxidase subunit 5B, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 98 amino acids
Theoretical weight: 10.63 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P10606 (Residues: 32-129; Coverage: 76%)
Gene name: COX5B
Sequence domains: Cytochrome c oxidase subunit Vb
Structure domains: Cytochrome c oxidase, subunit Vb
Cytochrome c oxidase subunit 6A1, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 75 amino acids
Theoretical weight: 8.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P12074 (Residues: 34-108; Coverage: 69%)
Gene names: COX6A1, COX6AL
Sequence domains: Cytochrome c oxidase subunit VIa
Structure domains: Cytochrome c oxidase, subunit VIa
Cytochrome c oxidase subunit 6B1 Chain: H
Molecule details ›
Chain: H
Length: 82 amino acids
Theoretical weight: 9.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P14854 (Residues: 5-86; Coverage: 95%)
Gene names: COX6B, COX6B1
Sequence domains: Cytochrome oxidase c subunit VIb
Structure domains: Cytochrome c oxidase, subunit VIb
Cytochrome c oxidase subunit 6C Chain: I
Molecule details ›
Chain: I
Length: 73 amino acids
Theoretical weight: 8.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09669 (Residues: 3-75; Coverage: 97%)
Gene name: COX6C
Sequence domains: Cytochrome c oxidase subunit VIc
Structure domains: Mitochondrial cytochrome c oxidase subunit VIc/VIIs
Cytochrome c oxidase subunit 7A2, mitochondrial Chain: J
Molecule details ›
Chain: J
Length: 56 amino acids
Theoretical weight: 6.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P14406 (Residues: 25-80; Coverage: 68%)
Gene names: COX7A2, COX7AL
Sequence domains: Cytochrome c oxidase subunit VII
Structure domains: Cytochrome c oxidase, subunit VIIa
Cytochrome c oxidase subunit 7B, mitochondrial Chain: K
Molecule details ›
Chain: K
Length: 49 amino acids
Theoretical weight: 5.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P24311 (Residues: 30-78; Coverage: 61%)
Gene name: COX7B
Sequence domains: Cytochrome C oxidase chain VIIB
Structure domains: Cytochrome C Oxidase, chain K
Cytochrome c oxidase subunit 7C, mitochondrial Chain: L
Molecule details ›
Chain: L
Length: 47 amino acids
Theoretical weight: 5.36 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15954 (Residues: 17-63; Coverage: 75%)
Gene name: COX7C
Sequence domains: Cytochrome c oxidase subunit VIIc
Structure domains: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 8A, mitochondrial Chain: M
Molecule details ›
Chain: M
Length: 43 amino acids
Theoretical weight: 4.77 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P10176 (Residues: 26-68; Coverage: 62%)
Gene names: COX8, COX8A, COX8L
Sequence domains: Cytochrome oxidase c subunit VIII
Structure domains: Cytochrome c oxidase, subunit 8
Cytochrome c oxidase subunit NDUFA4 Chain: N
Molecule details ›
Chain: N
Length: 79 amino acids
Theoretical weight: 9.14 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00483 (Residues: 3-81; Coverage: 98%)
Gene name: NDUFA4
Sequence domains: NADH-ubiquinone reductase complex 1 MLRQ subunit

Ligands and Environments

6 bound ligands:
Ligand CU 3 x CU
Ligand MG 1 x MG
Ligand HEA 2 x HEA
Ligand PEE 3 x PEE
Ligand CDL 1 x CDL
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-6896

Quick links

Citations

27 review citations

Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome.
Hock et al. (2020)
26 more

39 mentions without citation

Getting out what you put in: Copper in mitochondria and its impacts on human disease.
Cobine et al. (2021)
38 more