› 6hu9

Electron Microscopy
3.35Å resolution

III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae

Released:
DOI: 10.2210/pdb6hu9/pdb
PDB entry 6hu9 coloured by chain, front view.
PDB entry 6hu9 coloured by chain, side view.
PDB entry 6hu9 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1.
Hartley AM, Lukoyanova N, Zhang Y, Cabrera-Orefice A, Arnold S, Meunier B, Pinotsis N, Maréchal A
Nat Struct Mol Biol 26 78-83 (2019)
PMID: 30598554
Related structures: EMD-0262

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 44-mer (preferred)
PDBe Complex ID:
PDB-CPX-132273 (preferred)
Entry contents:
22 distinct polypeptide molecules
Macromolecules (22 distinct):
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:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
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)
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
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:
Structure domains: Cytochrome Bc1 Complex; Chain C
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
Structure domains:
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:
Structure domains:
Cytochrome b-c1 complex subunit 6, mitochondrial Chains: F, Q
Molecule details ›
Chains: F, Q
Length: 147 amino acids
Theoretical weight: 17.28 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00127 (Residues: 1-147; Coverage: 100%)
Gene names: QCR6, UCR6, YFR033C
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Structure domains: Ubiquinol-cytochrome C reductase hinge domain
Cytochrome b-c1 complex subunit 7, mitochondrial Chains: G, R
Molecule details ›
Chains: G, R
Length: 127 amino acids
Theoretical weight: 14.58 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00128 (Residues: 1-127; Coverage: 100%)
Gene names: CRO1, D9719.32, QCR7, UCR7, YDR529C
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Structure domains: Cytochrome b-c1 complex subunit 7
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
Structure domains: Cytochrome b-c1 complex subunit 8
Cytochrome b-c1 complex subunit 9, mitochondrial Chains: I, T
Molecule details ›
Chains: I, T
Length: 66 amino acids
Theoretical weight: 7.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22289 (Residues: 1-66; Coverage: 100%)
Gene names: QCR9, UCR9, YGR183C
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Structure domains: Cytochrome b-c1 complex subunit 9
Cytochrome b-c1 complex subunit 10, mitochondrial Chains: J, U
Molecule details ›
Chains: J, U
Length: 77 amino acids
Theoretical weight: 8.6 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P37299 (Residues: 1-77; Coverage: 100%)
Gene names: QCR10, YHR001BW, YHR001W-A
Sequence domains: Ubiquinol-cytochrome-c reductase complex subunit (QCR10)
Cytochrome c oxidase subunit 1 Chains: a, m
Molecule details ›
Chains: a, m
Length: 534 amino acids
Theoretical weight: 58.83 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00401 (Residues: 1-534; Coverage: 100%)
Gene names: COX1, OXI3, Q0045
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, n
Molecule details ›
Chains: b, n
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:
Structure domains:
Cytochrome c oxidase subunit 3 Chains: c, o
Molecule details ›
Chains: c, o
Length: 269 amino acids
Theoretical weight: 30.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00420 (Residues: 1-269; Coverage: 100%)
Gene names: COX3, OXI2, Q0275
Sequence domains: Cytochrome c oxidase subunit III
Structure domains:
Cytochrome c oxidase subunit 4, mitochondrial Chains: d, p
Molecule details ›
Chains: d, p
Length: 130 amino acids
Theoretical weight: 14.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04037 (Residues: 26-155; Coverage: 84%)
Gene names: COX4, G1362, YGL187C
Sequence domains: Cytochrome c oxidase subunit Vb
Cytochrome c oxidase subunit 5A, mitochondrial Chains: e, q
Molecule details ›
Chains: e, q
Length: 133 amino acids
Theoretical weight: 14.89 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00424 (Residues: 21-153; Coverage: 87%)
Gene names: COX5A, N2474, YNL052W, YNL2474W
Sequence domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 6, mitochondrial Chains: f, r
Molecule details ›
Chains: f, r
Length: 108 amino acids
Theoretical weight: 12.64 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00427 (Residues: 41-148; Coverage: 73%)
Gene names: COX6, YHR051W
Sequence domains: Cytochrome c oxidase subunit Va
Structure domains: Cytochrome c oxidase, subunit Va/VI
Cytochrome c oxidase subunit 7, mitochondrial Chains: g, s
Molecule details ›
Chains: g, s
Length: 59 amino acids
Theoretical weight: 6.81 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P10174 (Residues: 2-60; Coverage: 98%)
Gene names: COX7, YM9920.10C, YMR256C
Sequence domains: Cytochrome c oxidase subunit VII
Cytochrome c oxidase subunit 8, mitochondrial Chains: h, t
Molecule details ›
Chains: h, t
Length: 47 amino acids
Theoretical weight: 5.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04039 (Residues: 28-74; Coverage: 60%)
Gene names: COX8, L8084.14, YLR395C
Sequence domains: Cytochrome c oxidase subunit VIIc
Structure domains: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 9, mitochondrial Chains: i, u
Molecule details ›
Chains: i, u
Length: 55 amino acids
Theoretical weight: 6.47 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P07255 (Residues: 2-56; Coverage: 93%)
Gene names: COX9, D2520, YDL067C
Cytochrome c oxidase subunit 12, mitochondrial Chains: j, v
Molecule details ›
Chains: j, v
Length: 82 amino acids
Theoretical weight: 9.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q01519 (Residues: 2-83; Coverage: 99%)
Gene names: COX12, YLR038C
Sequence domains: Cytochrome oxidase c subunit VIb
Structure domains: Cytochrome c oxidase, subunit VIb
Cytochrome c oxidase subunit 13, mitochondrial Chains: k, w
Molecule details ›
Chains: k, w
Length: 131 amino acids
Theoretical weight: 15.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32799 (Residues: 10-129; Coverage: 93%)
Gene names: COX13, G1341, YGL191W
Sequence domains: Cytochrome c oxidase subunit VIa
Cytochrome c oxidase subunit 26, mitochondrial Chains: l, x
Molecule details ›
Chains: l, x
Length: 66 amino acids
Theoretical weight: 7.46 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q2V2P9 (Residues: 1-66; Coverage: 100%)
Gene names: COX26, YDR119W-A

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM

Cofactor: Ligand HEA 4 x HEA

Cofactor: Ligand HEC 2 x HEC
10 bound ligands:
Ligand PEF 28 x PEF
Ligand UQ6 1 x UQ6
Ligand CDL 8 x CDL
Ligand PCF 8 x PCF
Ligand FES 2 x FES
Ligand CU 2 x CU
Ligand CA 2 x CA
Ligand MG 2 x MG
Ligand CUA 4 x CUA
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.35Å
Relevant EMDB volumes: EMD-0262
Expression system: Saccharomyces cerevisiae

Quick links

Citations

15 review citations

The assembly, regulation and function of the mitochondrial respiratory chain.
Vercellino et al. (2022)
14 more

20 mentions without citation

Coordination chemistry of mitochondrial copper metalloenzymes: exploring implications for copper dyshomeostasis in cell death.
Shim et al. (2023)
19 more