› 5wau

X-ray diffraction
1.95Å resolution

Crystal Structure of CO-bound Cytochrome c Oxidase determined by Synchrotron X-Ray Crystallography at 100 K

Released:
DOI: 10.2210/pdb5wau/pdb
PDB entry 5wau coloured by chain, front view.
PDB entry 5wau coloured by chain, side view.
PDB entry 5wau coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature.
Ishigami I, Zatsepin NA, Hikita M, Conrad CE, Nelson G, Coe JD, Basu S, Grant TD, Seaberg MH, Sierra RG, Hunter MS, Fromme P, Fromme R, Yeh SR, Rousseau DL
Proc Natl Acad Sci U S A 114 8011-8016 (2017)
PMID: 28698372

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 26-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132470 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
Cytochrome c oxidase subunit 1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 514 amino acids
Theoretical weight: 57.09 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00396 (Residues: 1-514; Coverage: 100%)
Gene names: COI, COXI, MT-CO1, MTCO1
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Structure domains: Cytochrome c oxidase-like, subunit I domain
Cytochrome c oxidase subunit 2 Chains: B, b
Molecule details ›
Chains: B, b
Length: 227 amino acids
Theoretical weight: 26.07 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P68530 (Residues: 1-227; Coverage: 100%)
Gene names: COII, COX2, COXII, MT-CO2, MTCO2
Sequence domains:
Structure domains:
Cytochrome c oxidase subunit 3 Chains: C, c
Molecule details ›
Chains: C, c
Length: 261 amino acids
Theoretical weight: 29.96 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00415 (Residues: 1-261; Coverage: 100%)
Gene names: COIII, COXIII, MT-CO3, MTCO3
Sequence domains: Cytochrome c oxidase subunit III
Structure domains:
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chains: D, d
Molecule details ›
Chains: D, d
Length: 147 amino acids
Theoretical weight: 17.18 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00423 (Residues: 23-169; Coverage: 87%)
Gene names: COX4, COX4I1
Sequence domains: Cytochrome c oxidase subunit IV
Structure domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 5A, mitochondrial Chains: E, e
Molecule details ›
Chains: E, e
Length: 109 amino acids
Theoretical weight: 12.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00426 (Residues: 44-152; Coverage: 72%)
Gene name: COX5A
Sequence domains: Cytochrome c oxidase subunit Va
Structure domains: Cytochrome c oxidase, subunit Va/VI
Cytochrome c oxidase subunit 5B, mitochondrial Chains: F, f
Molecule details ›
Chains: F, f
Length: 98 amino acids
Theoretical weight: 10.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00428 (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 6A2, mitochondrial Chains: G, g
Molecule details ›
Chains: G, g
Length: 85 amino acids
Theoretical weight: 9.63 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07471 (Residues: 13-97; Coverage: 88%)
Gene names: COX6A, COX6A2
Sequence domains: Cytochrome c oxidase subunit VIa
Structure domains: Cytochrome c oxidase, subunit VIa
Cytochrome c oxidase subunit 6B1 Chains: H, h
Molecule details ›
Chains: H, h
Length: 85 amino acids
Theoretical weight: 10.04 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00429 (Residues: 2-86; Coverage: 99%)
Gene names: COX6B, COX6B1
Sequence domains: Cytochrome oxidase c subunit VIb
Structure domains: Cytochrome c oxidase, subunit VIb
Cytochrome c oxidase subunit 6C Chains: I, i
Molecule details ›
Chains: I, i
Length: 73 amino acids
Theoretical weight: 8.54 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P04038 (Residues: 2-74; Coverage: 99%)
Gene name: COX6C
Sequence domains: Cytochrome c oxidase subunit VIc
Structure domains: Mitochondrial cytochrome c oxidase subunit VIc/VIIs
Cytochrome c oxidase subunit 7A1, mitochondrial Chains: J, j
Molecule details ›
Chains: J, j
Length: 59 amino acids
Theoretical weight: 6.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07470 (Residues: 22-80; Coverage: 74%)
Gene names: COX7A, COX7A1, COX7AH
Sequence domains: Cytochrome c oxidase subunit VII
Structure domains: Cytochrome c oxidase, subunit VIIa
Cytochrome c oxidase subunit 7B, mitochondrial Chains: K, k
Molecule details ›
Chains: K, k
Length: 56 amino acids
Theoretical weight: 6.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13183 (Residues: 25-80; Coverage: 70%)
Gene name: COX7B
Sequence domains: Cytochrome C oxidase chain VIIB
Structure domains: Cytochrome C Oxidase, chain K
Cytochrome c oxidase subunit 7C, mitochondrial Chains: L, l
Molecule details ›
Chains: L, l
Length: 47 amino acids
Theoretical weight: 5.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00430 (Residues: 17-63; Coverage: 75%)
Gene names: COX7C, COX7CP1
Sequence domains: Cytochrome c oxidase subunit VIIc
Structure domains: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 8B, mitochondrial Chains: M, m
Molecule details ›
Chains: M, m
Length: 46 amino acids
Theoretical weight: 4.97 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P10175 (Residues: 25-70; Coverage: 66%)
Gene names: COX8B, COX8H
Sequence domains: Cytochrome oxidase c subunit VIII
Structure domains: Cytochrome c oxidase, subunit 8

Ligands and Environments

14 bound ligands:
Ligand HEA 4 x HEA
Ligand CU 2 x CU
Ligand MG 2 x MG
Ligand NA 2 x NA
Ligand PGV 8 x PGV
Ligand TGL 6 x TGL
Ligand CMO 2 x CMO
Ligand CUA 2 x CUA
Ligand CHD 8 x CHD
Ligand PEK 6 x PEK
Ligand CDL 4 x CDL
Ligand DMU 4 x DMU
Ligand PSC 2 x PSC
Ligand ZN 2 x ZN
3 modified residues:
Ligand FME 4 x FME
Ligand TPO 2 x TPO
Ligand SAC 2 x SAC

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P212121
Unit cell:
a: 177.923Å b: 182.555Å c: 208.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.217 0.244

Quick links

Citations

10 review citations

Mitochondrial Structure and Bioenergetics in Normal and Disease Conditions.
Protasoni et al. (2021)
9 more

5 mentions without citation

Why All the Fuss about Oxidative Phosphorylation (OXPHOS)?
Xu et al. (2020)
4 more