› 6ymx

Electron Microscopy
3.17Å resolution

CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae

Released:
DOI: 10.2210/pdb6ymx/pdb
PDB entry 6ymx coloured by chain, front view.
PDB entry 6ymx coloured by chain, side view.
PDB entry 6ymx coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance.
Berndtsson J, Aufschnaiter A, Rathore S, Marin-Buera L, Dawitz H, Diessl J, Kohler V, Barrientos A, Büttner S, Fontanesi F, Ott M
EMBO Rep 21 e51015 (2020)
PMID: 33016568
Related structures: EMD-10847

Function and Biology Details

Reactions catalysed: 
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Quinol + 2 ferricytochrome c(Side 2) = quinone + 2 ferrocytochrome c(Side 2) + 2 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-132269 (preferred)
Entry contents:
25 distinct polypeptide molecules
Macromolecules (25 distinct):
Cytochrome c oxidase subunit 1 Chain: a
Molecule details ›
Chain: a
Length: 530 amino acids
Theoretical weight: 58.32 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00401 (Residues: 5-534; Coverage: 99%)
Gene names: COX1, OXI3, Q0045
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Cytochrome c oxidase subunit 2 Chain: b
Molecule details ›
Chain: b
Length: 236 amino acids
Theoretical weight: 26.78 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00410 (Residues: 16-251; Coverage: 94%)
Gene names: COX2, OXI1, Q0250
Sequence domains:
Cytochrome c oxidase subunit 3 Chain: c
Molecule details ›
Chain: c
Length: 268 amino acids
Theoretical weight: 30.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00420 (Residues: 2-269; Coverage: 100%)
Gene names: COX3, OXI2, Q0275
Sequence domains: Cytochrome c oxidase subunit III
Cytochrome c oxidase subunit 4, mitochondrial Chain: d
Molecule details ›
Chain: d
Length: 117 amino acids
Theoretical weight: 12.69 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04037 (Residues: 30-146; Coverage: 76%)
Gene names: COX4, G1362, YGL187C
Sequence domains: Cytochrome c oxidase subunit Vb
Cytochrome c oxidase subunit 5A, mitochondrial Chain: e
Molecule details ›
Chain: e
Length: 128 amino acids
Theoretical weight: 14.32 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00424 (Residues: 25-152; Coverage: 84%)
Gene names: COX5A, N2474, YNL052W, YNL2474W
Sequence domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 6, mitochondrial Chain: f
Molecule details ›
Chain: f
Length: 99 amino acids
Theoretical weight: 11.73 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00427 (Residues: 47-145; Coverage: 67%)
Gene names: COX6, YHR051W
Sequence domains: Cytochrome c oxidase subunit Va
Cytochrome c oxidase subunit 7, mitochondrial Chain: g
Molecule details ›
Chain: g
Length: 55 amino acids
Theoretical weight: 6.41 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P10174 (Residues: 3-57; Coverage: 92%)
Gene names: COX7, YM9920.10C, YMR256C
Sequence domains: Cytochrome c oxidase subunit VII
Cytochrome c oxidase subunit 8, mitochondrial Chain: h
Molecule details ›
Chain: h
Length: 51 amino acids
Theoretical weight: 5.74 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04039 (Residues: 28-78; Coverage: 65%)
Gene names: COX8, L8084.14, YLR395C
Sequence domains: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 9, mitochondrial Chain: i
Molecule details ›
Chain: i
Length: 53 amino acids
Theoretical weight: 6.24 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P07255 (Residues: 3-55; Coverage: 90%)
Gene names: COX9, D2520, YDL067C
Cytochrome c oxidase subunit 12, mitochondrial Chain: j
Molecule details ›
Chain: j
Length: 78 amino acids
Theoretical weight: 9.23 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q01519 (Residues: 6-83; Coverage: 94%)
Gene names: COX12, YLR038C
Sequence domains: Cytochrome oxidase c subunit VIb
Cytochrome c oxidase subunit 13, mitochondrial Chain: k
Molecule details ›
Chain: k
Length: 114 amino acids
Theoretical weight: 13.31 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32799 (Residues: 16-129; Coverage: 88%)
Gene names: COX13, G1341, YGL191W
Sequence domains: Cytochrome c oxidase subunit VIa
Cytochrome c oxidase subunit 26, mitochondrial Chain: m
Molecule details ›
Chain: m
Length: 38 amino acids
Theoretical weight: 4.35 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q2V2P9 (Residues: 26-63; Coverage: 58%)
Gene names: COX26, YDR119W-A
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: A, L
Molecule details ›
Chains: A, L
Length: 431 amino acids
Theoretical weight: 47.46 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P07256 (Residues: 27-457; Coverage: 94%)
Gene names: COR1, QCR1, YBL0403, YBL045C
Sequence domains:
Cytochrome b-c1 complex subunit 2, mitochondrial Chains: B, M
Molecule details ›
Chains: B, M
Length: 352 amino acids
Theoretical weight: 38.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P07257 (Residues: 17-368; Coverage: 96%)
Gene names: COR2, P9677.6, QCR2, UCR2, YPR191W
Sequence domains: Insulinase (Peptidase family M16)
Cytochrome b Chains: C, N
Molecule details ›
Chains: C, N
Length: 385 amino acids
Theoretical weight: 43.69 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00163 (Residues: 1-385; Coverage: 100%)
Gene names: COB, CYTB, Q0105
Sequence domains:
Cytochrome c1, heme protein, mitochondrial Chains: D, O
Molecule details ›
Chains: D, O
Length: 248 amino acids
Theoretical weight: 27.81 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P07143 (Residues: 62-309; Coverage: 80%)
Gene names: CTC1, CYT1, YOR065W, YOR29-16
Sequence domains: Cytochrome C1 family
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: E, P
Molecule details ›
Chains: E, P
Length: 185 amino acids
Theoretical weight: 20.12 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P08067 (Residues: 31-215; Coverage: 86%)
Gene names: RIP1, YEL024W
Sequence domains:
Cytochrome b-c1 complex subunit 6, mitochondrial Chain: F
Molecule details ›
Chain: F
Length: 74 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00127 (Residues: 74-147; Coverage: 50%)
Gene names: QCR6, UCR6, YFR033C
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Cytochrome b-c1 complex subunit 7, mitochondrial Chains: G, R
Molecule details ›
Chains: G, R
Length: 126 amino acids
Theoretical weight: 14.45 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00128 (Residues: 2-127; Coverage: 99%)
Gene names: CRO1, D9719.32, QCR7, UCR7, YDR529C
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Cytochrome b-c1 complex subunit 8, mitochondrial Chains: H, S
Molecule details ›
Chains: H, S
Length: 93 amino acids
Theoretical weight: 10.86 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P08525 (Residues: 2-94; Coverage: 99%)
Gene names: J0526, QCR8, YJL166W
Sequence domains: UcrQ family
Cytochrome b-c1 complex subunit 9, mitochondrial Chain: I
Molecule details ›
Chain: I
Length: 54 amino acids
Theoretical weight: 6.21 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22289 (Residues: 5-58; Coverage: 82%)
Gene names: QCR9, UCR9, YGR183C
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Cytochrome b-c1 complex subunit 6, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 75 amino acids
Theoretical weight: 8.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00127 (Residues: 73-147; Coverage: 51%)
Gene names: QCR6, UCR6, YFR033C
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Cytochrome b-c1 complex subunit 9, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 54 amino acids
Theoretical weight: 6.23 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22289 (Residues: 4-57; Coverage: 82%)
Gene names: QCR9, UCR9, YGR183C
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Cytochrome b-c1 complex subunit 10, mitochondrial Chain: U
Molecule details ›
Chain: U
Length: 44 amino acids
Theoretical weight: 4.92 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P37299 (Residues: 10-53; Coverage: 57%)
Gene names: QCR10, YHR001BW, YHR001W-A
Sequence domains: Ubiquinol-cytochrome-c reductase complex subunit (QCR10)
Cytochrome b-c1 complex subunit 10, mitochondrial Chain: V
Molecule details ›
Chain: V
Length: 51 amino acids
Theoretical weight: 5.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P37299 (Residues: 11-61; Coverage: 66%)
Gene names: QCR10, YHR001BW, YHR001W-A
Sequence domains: Ubiquinol-cytochrome-c reductase complex subunit (QCR10)

Ligands and Environments

15 bound ligands:
Ligand CU 1 x CU
Ligand HEA 2 x HEA
Ligand PTY 7 x PTY
Ligand CN3 2 x CN3
Ligand CUA 1 x CUA
Ligand PCF 5 x PCF
Ligand ZN 1 x ZN
Ligand 6PH 2 x 6PH
Ligand HEM 6 x HEM
Ligand 8PE 2 x 8PE
Ligand CN5 1 x CN5
Ligand UQ6 2 x UQ6
Ligand 9PE 2 x 9PE
Ligand 7PH 2 x 7PH
Ligand FES 2 x FES
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.17Å
Relevant EMDB volumes: EMD-10847

Quick links

Citations

13 review citations

Molecular and Supramolecular Structure of the Mitochondrial Oxidative Phosphorylation System: Implications for Pathology.
Nesci et al. (2021)
12 more

3 mentions without citation

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