› 7vuw

X-ray diffraction
1.6Å resolution

Bovine heart cytochrome c oxidase in the cyanide-bound fully oxidized state at 50 K

Released:
DOI: 10.2210/pdb7vuw/pdb
Model geometry
Fit model/data
PDB entry 7vuw coloured by chain, front view.
PDB entry 7vuw coloured by chain, side view.
PDB entry 7vuw coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons.
Shimada A, Baba J, Nagao S, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S
OpenAccess logo J Biol Chem 299 105277 (2023)
PMID: 37742916

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 tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132466 (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
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chains: D, Q
Cytochrome c oxidase subunit 5A, mitochondrial Chains: E, R
Cytochrome c oxidase subunit 5B, mitochondrial Chains: F, S
Cytochrome c oxidase subunit 6A2, mitochondrial Chains: G, T
Cytochrome c oxidase subunit 6B1 Chains: H, U
Cytochrome c oxidase subunit 6C Chains: I, V
Cytochrome c oxidase subunit 7A1, mitochondrial Chains: J, W
Cytochrome c oxidase subunit 7B, mitochondrial Chains: K, X
Cytochrome c oxidase subunit 7C, mitochondrial Chains: L, Y
Cytochrome c oxidase subunit 8B, mitochondrial Chains: M, Z

Ligands and Environments

16 bound ligands:
Ligand HEA 4 x HEA
Ligand CU 2 x CU
Ligand MG 2 x MG
Ligand NA 2 x NA
Ligand CYN 2 x CYN
Ligand PGV 8 x PGV
Ligand EDO 249 x EDO
Ligand TGL 6 x TGL
Ligand CUA 2 x CUA
Ligand PSC 2 x PSC
Ligand CHD 7 x CHD
Ligand PEK 6 x PEK
Ligand CDL 4 x CDL
Ligand DMU 14 x DMU
Ligand ZN 2 x ZN
Ligand PO4 2 x PO4
3 modified residues:
Ligand FME 4 x FME
Ligand TPO 2 x TPO
Ligand SAC 2 x SAC

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 182.076Å b: 204.481Å c: 177.68Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.154 0.175

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