› 6t0b

Electron Microscopy
2.8Å resolution

The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae

Released:
DOI: 10.2210/pdb6t0b/pdb
PDB entry 6t0b coloured by chain, front view.
PDB entry 6t0b coloured by chain, side view.
PDB entry 6t0b coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes.
Hartley AM, Meunier B, Pinotsis N, Maréchal A
Proc Natl Acad Sci U S A 117 9329-9337 (2020)
PMID: 32291341
Related structures: EMD-10340

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 46-mer (preferred)
PDBe Complex ID:
PDB-CPX-132274 (preferred)
Entry contents:
23 distinct polypeptide molecules
Macromolecules (23 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:
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 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
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
Cytochrome b-c1 complex subunit 8, mitochondrial Chains: H, S
Molecule details ›
Chains: H, S
Length: 94 amino acids
Theoretical weight: 10.99 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P08525 (Residues: 1-94; Coverage: 100%)
Gene names: J0526, QCR8, YJL166W
Sequence domains: UcrQ family
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
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, n
Molecule details ›
Chains: a, n
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
Cytochrome c oxidase subunit 2 Chains: b, o
Molecule details ›
Chains: b, o
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 Chains: c, p
Molecule details ›
Chains: c, p
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
Cytochrome c oxidase subunit 4, mitochondrial Chains: d, q
Molecule details ›
Chains: d, q
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 5B, mitochondrial Chains: e, r
Molecule details ›
Chains: e, r
Length: 134 amino acids
Theoretical weight: 15.33 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P00425 (Residues: 18-151; Coverage: 89%)
Gene names: COX5B, YIL111W
Sequence domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 6, mitochondrial Chains: f, s
Molecule details ›
Chains: f, s
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
Cytochrome c oxidase subunit 7, mitochondrial Chains: g, t
Molecule details ›
Chains: g, t
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, u
Molecule details ›
Chains: h, u
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 Chains: i, v
Molecule details ›
Chains: i, v
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, w
Molecule details ›
Chains: j, w
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
Cytochrome c oxidase subunit 13, mitochondrial Chains: k, x
Molecule details ›
Chains: k, x
Length: 131 amino acids
Theoretical weight: 15.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
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, y
Molecule details ›
Chains: l, y
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
Respiratory supercomplex factor 2, mitochondrial Chains: m, z
Molecule details ›
Chains: m, z
Length: 224 amino acids
Theoretical weight: 25.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53721 (Residues: 1-224; Coverage: 100%)
Gene names: AIM38, N3185, RCF2, YNR018W
Sequence domains: Hypoxia induced protein conserved region

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM

Cofactor: Ligand HEA 4 x HEA

Cofactor: Ligand HEC 2 x HEC
9 bound ligands:
Ligand CDL 8 x CDL
Ligand PEF 26 x PEF
Ligand PCF 7 x PCF
Ligand FES 2 x FES
Ligand CU 2 x CU
Ligand CA 2 x CA
Ligand MG 2 x MG
Ligand CUA 2 x CUA
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-10340
Expression system: Saccharomyces cerevisiae S288C

Quick links

Citations

8 review citations

HIGD-Driven Regulation of Cytochrome c Oxidase Biogenesis and Function.
Timón-Gómez et al. (2020)
7 more

4 mentions without citation

Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications.
Sun et al. (2023)
3 more