› 2yev

X-ray diffraction
2.36Å resolution

Structure of caa3-type cytochrome oxidase

Released:
DOI: 10.2210/pdb2yev/pdb
PDB entry 2yev coloured by chain, front view.
PDB entry 2yev coloured by chain, side view.
PDB entry 2yev coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Structural insights into electron transfer in caa3-type cytochrome oxidase.
Lyons JA, Aragão D, Slattery O, Pisliakov AV, Soulimane T, Caffrey M
Nature 487 514-8 (2012)
PMID: 22763450

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 trimer (preferred)
PDBe Complex ID:
PDB-CPX-161339 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Cytochrome c oxidase polypeptide I+III Chains: A, D
Molecule details ›
Chains: A, D
Length: 791 amino acids
Theoretical weight: 89.28 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P98005 (Residues: 1-791; Coverage: 100%)
Gene names: TTHA0312, caaA, ctaD
Sequence domains:
Structure domains:
Cytochrome c oxidase subunit 2 Chains: B, E
Molecule details ›
Chains: B, E
Length: 337 amino acids
Theoretical weight: 37.39 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLI2 (Residues: 1-337; Coverage: 100%)
Gene name: TTHA0311
Sequence domains:
Structure domains:
Cytochrome oxidase Caa3-type subunit IV domain-containing protein Chains: C, F
Molecule details ›
Chains: C, F
Length: 66 amino acids
Theoretical weight: 7.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SH67 (Residues: 1-66; Coverage: 100%)
Gene name: TTHA1863
Sequence domains: CAA3-type cytochrome c oxidase subunit IV
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1

Ligands and Environments


Cofactor: Ligand HAS 4 x HAS

Cofactor: Ligand HEC 2 x HEC
8 bound ligands:
Ligand 5PL 2 x 5PL
Ligand CU 2 x CU
Ligand 4AG 1 x 4AG
Ligand 7E8 2 x 7E8
Ligand MG 2 x MG
Ligand CUA 2 x CUA
Ligand 7E9 1 x 7E9
Ligand CL 3 x CL
1 modified residue:
Ligand FME 2 x FME

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B, DIAMOND BEAMLINE I24
Unit cell:
a: 127.25Å b: 76.03Å c: 300.267Å
α: 90° β: 92.21° γ: 90°
R-values:
R R work R free
0.174 0.171 0.218

Quick links

Citations

11 review citations

Copper active sites in biology.
Solomon et al. (2014)
10 more

17 mentions without citation

Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins.
Huang et al. (2018)
16 more