› 7thu

X-ray diffraction
1.93Å resolution

Structure of reduced bovine cytochrome c oxidase at 1.93 Angstrom resolution obtained by synchrotron X-rays

Released:
DOI: 10.2210/pdb7thu/pdb
PDB entry 7thu coloured by chain, front view.
PDB entry 7thu coloured by chain, side view.
PDB entry 7thu coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Temperature-dependent structural transition following X-ray-induced metal center reduction in oxidized cytochrome c oxidase.
Ishigami I, Russi S, Cohen A, Yeh SR, Rousseau DL
OpenAccess logo J Biol Chem 298 101799 (2022)
PMID: 35257742

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, N
Molecule details ›
Chains: A, N
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
Cytochrome c oxidase subunit 2 Chains: B, O
Molecule details ›
Chains: B, O
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:
Cytochrome c oxidase subunit 3 Chains: C, P
Molecule details ›
Chains: C, P
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
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chains: D, Q
Molecule details ›
Chains: D, Q
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
Cytochrome c oxidase subunit 5A, mitochondrial Chains: E, R
Molecule details ›
Chains: E, R
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
Cytochrome c oxidase subunit 5B, mitochondrial Chains: F, S
Molecule details ›
Chains: F, S
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
Cytochrome c oxidase subunit 6A2, mitochondrial Chains: G, T
Molecule details ›
Chains: G, T
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
Cytochrome c oxidase subunit 6B1 Chains: H, U
Molecule details ›
Chains: H, U
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
Cytochrome c oxidase subunit 6C Chains: I, V
Molecule details ›
Chains: I, V
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
Cytochrome c oxidase subunit 7A1, mitochondrial Chains: J, W
Molecule details ›
Chains: J, W
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
Cytochrome c oxidase subunit 7B, mitochondrial Chains: K, X
Molecule details ›
Chains: K, X
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
Cytochrome c oxidase subunit 7C, mitochondrial Chains: L, Y
Molecule details ›
Chains: L, Y
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
Cytochrome c oxidase subunit 8B, mitochondrial Chains: M, Z
Molecule details ›
Chains: M, Z
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

Ligands and Environments

15 bound ligands:
Ligand CU 2 x CU
Ligand MG 2 x MG
Ligand NA 2 x NA
Ligand PGV 8 x PGV
Ligand HEA 4 x HEA
Ligand EDO 91 x EDO
Ligand TGL 6 x TGL
Ligand CUA 2 x CUA
Ligand CHD 10 x CHD
Ligand DMU 6 x DMU
Ligand PEK 6 x PEK
Ligand CDL 4 x CDL
Ligand PSC 2 x PSC
Ligand ZN 2 x ZN
Ligand SAC 2 x SAC
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: APS BEAMLINE 31-ID
Spacegroup: P212121
Unit cell:
a: 178.182Å b: 182.282Å c: 208.683Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.184 0.212

Quick links

Citations

2 review citations

Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography.
Makita et al. (2023)
1 more

4 mentions without citation

Temperature-dependent structural transition following X-ray-induced metal center reduction in oxidized cytochrome c oxidase.
Ishigami et al. (2022)
3 more