› 7qhm

Electron Microscopy
2.8Å resolution

Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium glutamicum (stigmatellin and azide bound)

Released:
DOI: 10.2210/pdb7qhm/pdb
PDB entry 7qhm coloured by chain, front view.
PDB entry 7qhm coloured by chain, side view.
PDB entry 7qhm coloured by chain, top view.
Source organism: Corynebacterium glutamicum ATCC 13032
Primary publication:
Structural basis for safe and efficient energy conversion in a respiratory supercomplex.
Kao WC, Ortmann de Percin Northumberland C, Cheng TC, Ortiz J, Durand A, von Loeffelholz O, Schilling O, Biniossek ML, Klaholz BP, Hunte C
Nat Commun 13 545 (2022)
PMID: 35087070
Related structures: EMD-13976

Function and Biology Details

Reactions catalysed: 
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
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)
PDBe Complex ID:
PDB-CPX-154654 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
Cytochrome bc1 complex Rieske iron-sulfur subunit Chains: A, N
Molecule details ›
Chains: A, N
Length: 408 amino acids
Theoretical weight: 45.23 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q79VE8 (Residues: 1-408; Coverage: 100%)
Gene names: Cgl2190, cg2404, qcrA
Sequence domains:
Cytochrome bc1 complex cytochrome b subunit Chains: B, O
Molecule details ›
Chains: B, O
Length: 539 amino acids
Theoretical weight: 59.86 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q79VE9 (Residues: 1-539; Coverage: 100%)
Gene names: Cgl2189, cg2403, qcrB
Sequence domains: Cytochrome b(N-terminal)/b6/petB
Cytochrome bc1 complex cytochrome c subunit Chains: C, P
Molecule details ›
Chains: C, P
Length: 283 amino acids
Theoretical weight: 29.9 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q8NNK5 (Residues: 1-283; Coverage: 100%)
Gene names: Cgl2191, cg2405, qcrC
Sequence domains:
Cytochrome c oxidase subunit 1 Chains: D, Q
Molecule details ›
Chains: D, Q
Length: 594 amino acids
Theoretical weight: 66.34 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q79VD7 (Residues: 1-584; Coverage: 100%)
Gene names: Cgl2523, cg2780, ctaD
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Cytochrome c oxidase subunit 2 Chains: E, R
Molecule details ›
Chains: E, R
Length: 331 amino acids
Theoretical weight: 36.81 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q8NNK2 (Residues: 29-359; Coverage: 100%)
Gene names: Cgl2195, cg2409, ctaC
Sequence domains: Cytochrome C oxidase subunit II, periplasmic domain
Cytochrome c oxidase subunit 3 Chains: F, S
Molecule details ›
Chains: F, S
Length: 205 amino acids
Theoretical weight: 22.46 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q9AEL8 (Residues: 1-205; Coverage: 100%)
Gene names: Cgl2192, cg2406, ctaE
Sequence domains: Cytochrome c oxidase subunit III
Cytochrome c oxidase polypeptide 4 Chains: G, T
Molecule details ›
Chains: G, T
Length: 143 amino acids
Theoretical weight: 15.56 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q8NNK3 (Residues: 1-143; Coverage: 100%)
Gene names: Cgl2194, cg2408, ctaF
Sequence domains: Cytochrome c oxidase subunit IV
P29 Chains: H, U
Molecule details ›
Chains: H, U
Length: 163 amino acids
Theoretical weight: 16.95 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q8NMB4 (Residues: 32-194; Coverage: 99%)
Gene names: Cgl2664, cg2949
Uncharacterized membrane protein Cgl2017/cg2211 Chains: I, V
Molecule details ›
Chains: I, V
Length: 147 amino acids
Theoretical weight: 16.39 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q8NP09 (Residues: 1-147; Coverage: 100%)
Gene names: Cgl2017, cg2211
Sequence domains: Protein of unknown function (DUF2631)
Hypothetical membrane protein Chains: J, W
Molecule details ›
Chains: J, W
Length: 112 amino acids
Theoretical weight: 12.14 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q8NTD4 (Residues: 1-112; Coverage: 100%)
Gene name: Cgl0373
Actinobacterial supercomplex, subunit C (AscC) Chains: K, X
Molecule details ›
Chains: K, X
Length: 73 amino acids
Theoretical weight: 8.37 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q8NS61 (Residues: 1-73; Coverage: 100%)
Gene name: Cgl0818
Hypothetical membrane protein Chains: L, Y
Molecule details ›
Chains: L, Y
Length: 65 amino acids
Theoretical weight: 6.63 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: Q8NSJ8 (Residues: 1-65; Coverage: 100%)
Gene name: Cgl0673
Thiamine biosynthesis protein X Chains: M, Z
Molecule details ›
Chains: M, Z
Length: 168 amino acids
Theoretical weight: 17.15 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Corynebacterium glutamicum ATCC 13032
UniProt:
  • Canonical: P42461 (Residues: 23-190; Coverage: 100%)
Gene names: Cgl2332, cg2561, thiX

Ligands and Environments

21 bound ligands:
Ligand FES 2 x FES
Ligand IZL 2 x IZL
Ligand 9YF 4 x 9YF
Ligand MQ9 4 x MQ9
Ligand 3PE 17 x 3PE
Ligand SMA 2 x SMA
Ligand HEM 4 x HEM
Ligand CDL 16 x CDL
Ligand LYC 2 x LYC
Ligand LMT 2 x LMT
Ligand HEC 4 x HEC
Ligand HAS 4 x HAS
Ligand CU 2 x CU
Ligand MN 2 x MN
Ligand CA 2 x CA
Ligand AZI 2 x AZI
Ligand CUA 4 x CUA
Ligand DGA 6 x DGA
Ligand PLM 4 x PLM
Ligand IX7 2 x IX7
Ligand OXY 1 x OXY
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-13976
Expression system: Corynebacterium glutamicum ATCC 13032

Quick links

Citations

3 review citations

The functional significance of mitochondrial respiratory chain supercomplexes.
Kohler et al. (2023)
2 more

2 mentions without citation

Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy.
Kao et al. (2022)
1 more