› 3omi

X-ray diffraction
2.15Å resolution

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with D132A mutation

Released:
DOI: 10.2210/pdb3omi/pdb
PDB entry 3omi coloured by chain, front view.
PDB entry 3omi coloured by chain, side view.
PDB entry 3omi coloured by chain, top view.
Source organism: Cereibacter sphaeroides 2.4.1
Primary publication:
Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.
Liu J, Qin L, Ferguson-Miller S
Proc Natl Acad Sci U S A 108 1284-9 (2011)
PMID: 21205904

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-174617 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cytochrome c oxidase subunit 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 535 amino acids
Theoretical weight: 59.5 KDa
Source organism: Cereibacter sphaeroides 2.4.1
Expression system: Cereibacter sphaeroides
UniProt:
  • Canonical: Q3J5A7 (Residues: 17-551; Coverage: 95%)
Gene names: RSP_1877, coxI
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: 256 amino acids
Theoretical weight: 28.62 KDa
Source organism: Cereibacter sphaeroides 2.4.1
Expression system: Cereibacter sphaeroides
UniProt:
  • Canonical: Q3J5G0 (Residues: 30-281; Coverage: 91%)
Gene names: RSP_1826, coxII
Sequence domains:
Structure domains:

Ligands and Environments

11 bound ligands:
Ligand OH 2 x OH
Ligand DMU 11 x DMU
Ligand TRD 9 x TRD
Ligand HEA 4 x HEA
Ligand CU 4 x CU
Ligand MG 2 x MG
Ligand CA 2 x CA
Ligand CL 2 x CL
Ligand HTH 1 x HTH
Ligand CU1 2 x CU1
Ligand CD 4 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 125.064Å b: 131.519Å c: 175.674Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.192 0.215
Expression system: Cereibacter sphaeroides

Quick links

Citations

7 review citations

Cellular and molecular mechanisms of mitochondrial function.
Osellame et al. (2012)
6 more

1 mention without citation

Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.
Liu et al. (2011)