› 3fye

X-ray diffraction
2.15Å resolution

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state

Released:
DOI: 10.2210/pdb3fye/pdb
PDB entry 3fye coloured by chain, front view.
PDB entry 3fye coloured by chain, side view.
PDB entry 3fye coloured by chain, top view.
Source organism: Cereibacter sphaeroides
Primary publication:
Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake.
Qin L, Liu J, Mills DA, Proshlyakov DA, Hiser C, Ferguson-Miller S
Biochemistry 48 5121-30 (2009)
PMID: 19397279

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152619 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cytochrome c oxidase subunit 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 566 amino acids
Theoretical weight: 63.2 KDa
Source organism: Cereibacter sphaeroides
Expression system: Cereibacter sphaeroides
UniProt:
  • Canonical: P33517 (Residues: 1-566; Coverage: 100%)
Gene name: ctaD
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, D
Molecule details ›
Chains: B, D
Length: 262 amino acids
Theoretical weight: 29.37 KDa
Source organism: Cereibacter sphaeroides
Expression system: Cereibacter sphaeroides
UniProt:
  • Canonical: Q03736 (Residues: 26-281; Coverage: 92%)
Gene names: coxII, ctaB, ctaC
Sequence domains:
Structure domains:

Ligands and Environments

9 bound ligands:
Ligand HEA 4 x HEA
Ligand CU1 6 x CU1
Ligand MG 2 x MG
Ligand CA 2 x CA
Ligand UNX 2 x UNX
Ligand DMU 10 x DMU
Ligand TRD 12 x TRD
Ligand HTO 1 x HTO
Ligand CD 4 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 124.613Å b: 131.472Å c: 176.192Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 0.221
Expression system: Cereibacter sphaeroides

Quick links

Citations

12 review citations

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

11 mentions without citation

Gating and regulation of the cytochrome c oxidase proton pump.
Ferguson-Miller et al. (2012)
10 more