› 6juw

X-ray diffraction
1.8Å resolution

BOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1.80 ANGSTROM RESOLUTION

Released:
DOI: 10.2210/pdb6juw/pdb
PDB entry 6juw coloured by chain, front view.
PDB entry 6juw coloured by chain, side view.
PDB entry 6juw coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
X-ray structures of catalytic intermediates of cytochrome c oxidase provide insights into its O2 activation and unidirectional proton-pump mechanisms.
Shimada A, Etoh Y, Kitoh-Fujisawa R, Sasaki A, Shinzawa-Itoh K, Hiromoto T, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S
J Biol Chem 295 5818-5833 (2020)
PMID: 32165497

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: 259 amino acids
Theoretical weight: 29.73 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00415 (Residues: 3-261; Coverage: 99%)
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: 144 amino acids
Theoretical weight: 16.91 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00423 (Residues: 26-169; Coverage: 85%)
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: 105 amino acids
Theoretical weight: 12.08 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00426 (Residues: 48-152; Coverage: 69%)
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: 84 amino acids
Theoretical weight: 9.53 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07471 (Residues: 13-96; Coverage: 87%)
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: 79 amino acids
Theoretical weight: 9.41 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00429 (Residues: 8-86; Coverage: 92%)
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: 58 amino acids
Theoretical weight: 6.55 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07470 (Residues: 22-79; Coverage: 73%)
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: 49 amino acids
Theoretical weight: 5.44 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13183 (Residues: 30-78; Coverage: 61%)
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: 46 amino acids
Theoretical weight: 5.36 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00430 (Residues: 18-63; Coverage: 73%)
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: 43 amino acids
Theoretical weight: 4.74 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P10175 (Residues: 25-67; Coverage: 61%)
Gene names: COX8B, COX8H
Sequence domains: Cytochrome oxidase c subunit VIII

Ligands and Environments

15 bound ligands:
Ligand HEA 4 x HEA
Ligand CU 2 x CU
Ligand MG 2 x MG
Ligand NA 4 x NA
Ligand DMU 25 x DMU
Ligand PGV 8 x PGV
Ligand PSC 2 x PSC
Ligand TGL 6 x TGL
Ligand EDO 80 x EDO
Ligand CUA 2 x CUA
Ligand CHD 9 x CHD
Ligand CDL 4 x CDL
Ligand PEK 6 x PEK
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

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 182.217Å b: 204.65Å c: 177.397Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.156 0.188

Quick links

Citations

4 review citations

Impact of Hydrogen Sulfide on Mitochondrial and Bacterial Bioenergetics.
Borisov et al. (2021)
3 more

1 mention without citation

X-ray structures of catalytic intermediates of cytochrome c oxidase provide insights into its O2 activation and unidirectional proton-pump mechanisms.
Shimada et al. (2020)