› 8d4t

Electron Microscopy
3.1Å resolution

Mammalian CIV with GDN bound

Released:
DOI: 10.2210/pdb8d4t/pdb
PDB entry 8d4t coloured by chain, front view.
PDB entry 8d4t coloured by chain, side view.
PDB entry 8d4t coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Structural basis of mammalian complex IV inhibition by steroids.
Di Trani JM, Moe A, Riepl D, Saura P, Kaila VRI, Brzezinski P, Rubinstein JL
Proc Natl Acad Sci U S A 119 e2205228119 (2022)
PMID: 35858451
Related structures: EMD-27196

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-132468 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
Cytochrome c oxidase subunit 1 Chain: N
Molecule details ›
Chain: N
Length: 513 amino acids
Theoretical weight: 56.96 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00396 (Residues: 1-513; Coverage: 100%)
Gene names: COI, COXI, MT-CO1, MTCO1
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Cytochrome c oxidase subunit 2 Chain: O
Molecule details ›
Chain: 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 Chain: P
Molecule details ›
Chain: P
Length: 258 amino acids
Theoretical weight: 29.59 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00415 (Residues: 4-261; Coverage: 99%)
Gene names: COIII, COXIII, MT-CO3, MTCO3
Sequence domains: Cytochrome c oxidase subunit III
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 137 amino acids
Theoretical weight: 16.15 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00423 (Residues: 32-168; Coverage: 81%)
Gene names: COX4, COX4I1
Sequence domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 5A, mitochondrial Chain: R
Molecule details ›
Chain: R
Length: 102 amino acids
Theoretical weight: 11.72 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00426 (Residues: 49-150; Coverage: 67%)
Gene name: COX5A
Sequence domains: Cytochrome c oxidase subunit Va
Cytochrome c oxidase subunit 5B, mitochondrial Chain: S
Molecule details ›
Chain: S
Length: 91 amino acids
Theoretical weight: 10.02 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00428 (Residues: 35-125; Coverage: 71%)
Gene name: COX5B
Sequence domains: Cytochrome c oxidase subunit Vb
Cytochrome c oxidase subunit 6A2, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 72 amino acids
Theoretical weight: 8.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07471 (Residues: 24-95; Coverage: 74%)
Gene names: COX6A, COX6A2
Sequence domains: Cytochrome c oxidase subunit VIa
Cytochrome c oxidase subunit 6B1 Chain: U
Molecule details ›
Chain: U
Length: 78 amino acids
Theoretical weight: 9.28 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00429 (Residues: 9-86; Coverage: 91%)
Gene names: COX6B, COX6B1
Sequence domains: Cytochrome oxidase c subunit VIb
Cytochrome c oxidase subunit 6C Chain: V
Molecule details ›
Chain: V
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P04038 (Residues: 5-74; Coverage: 95%)
Gene name: COX6C
Sequence domains: Cytochrome c oxidase subunit VIc
Cytochrome c oxidase subunit 7A1, mitochondrial Chain: W
Molecule details ›
Chain: W
Length: 55 amino acids
Theoretical weight: 6.19 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07470 (Residues: 22-76; Coverage: 69%)
Gene names: COX7A, COX7A1, COX7AH
Sequence domains: Cytochrome c oxidase subunit VII
Cytochrome c oxidase subunit 7B, mitochondrial Chain: X
Molecule details ›
Chain: X
Length: 47 amino acids
Theoretical weight: 5.27 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13183 (Residues: 32-78; Coverage: 59%)
Gene name: COX7B
Sequence domains: Cytochrome C oxidase chain VIIB
Cytochrome c oxidase subunit 7C, mitochondrial Chain: Y
Molecule details ›
Chain: 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 8A, mitochondrial Chain: M
Molecule details ›
Chain: M
Length: 43 amino acids
Theoretical weight: 4.77 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P10176 (Residues: 26-68; Coverage: 62%)
Gene names: COX8, COX8A, COX8L
Sequence domains: Cytochrome oxidase c subunit VIII

Ligands and Environments

8 bound ligands:
Ligand CU 3 x CU
Ligand MG 1 x MG
Ligand NA 1 x NA
Ligand HEA 2 x HEA
Ligand PGV 2 x PGV
Ligand PEK 1 x PEK
Ligand 9Z9 1 x 9Z9
Ligand ZN 1 x ZN
1 modified residue:
Ligand FME 2 x FME

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-27196

Quick links

Citations

1 review citation

Interaction of Terminal Oxidases with Amphipathic Molecules.
Azarkina et al. (2023)
3 other articles