› 8ec0

Electron Microscopy
3.3Å resolution

III2IV respiratory supercomplex from Saccharomyces cerevisiae cardiolipin-lacking mutant

Released:
DOI: 10.2210/pdb8ec0/pdb
PDB entry 8ec0 coloured by chain, front view.
PDB entry 8ec0 coloured by chain, side view.
PDB entry 8ec0 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural insights into cardiolipin replacement by phosphatidylglycerol in a cardiolipin-lacking yeast respiratory supercomplex.
Hryc CF, Mallampalli VKPS, Bovshik EI, Azinas S, Fan G, Serysheva II, Sparagna GC, Baker ML, Mileykovskaya E, Dowhan W
OpenAccess logo Nat Commun 14 2783 (2023)
PMID: 37188665
Related structures: EMD-28011

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:

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
PDBe Complex ID:
PDB-CPX-216252 (preferred)
Entry contents:
21 distinct polypeptide molecules
Macromolecules (21 distinct):
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: A, a
Molecule details ›
Chains: A, a
Length: 457 amino acids
Theoretical weight: 50.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07256 (Residues: 1-457; Coverage: 100%)
Gene names: COR1, QCR1, YBL0403, YBL045C
Sequence domains:
Cytochrome b-c1 complex subunit 2, mitochondrial Chains: B, b
Molecule details ›
Chains: B, b
Length: 368 amino acids
Theoretical weight: 40.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07257 (Residues: 1-368; Coverage: 100%)
Gene names: COR2, P9677.6, QCR2, UCR2, YPR191W
Sequence domains: Insulinase (Peptidase family M16)
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: C, c
Molecule details ›
Chains: C, c
Length: 215 amino acids
Theoretical weight: 23.39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08067 (Residues: 1-215; Coverage: 100%)
Gene names: RIP1, YEL024W
Sequence domains:
Cytochrome b-c1 complex subunit 9, mitochondrial Chains: E, e
Molecule details ›
Chains: E, e
Length: 66 amino acids
Theoretical weight: 7.49 KDa
Source organism: Saccharomyces cerevisiae
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 7, mitochondrial Chains: F, f
Molecule details ›
Chains: F, f
Length: 127 amino acids
Theoretical weight: 14.58 KDa
Source organism: Saccharomyces cerevisiae
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 6, mitochondrial Chains: G, g
Molecule details ›
Chains: G, g
Length: 147 amino acids
Theoretical weight: 17.28 KDa
Source organism: Saccharomyces cerevisiae
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 8, mitochondrial Chains: H, h
Molecule details ›
Chains: H, h
Length: 94 amino acids
Theoretical weight: 10.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08525 (Residues: 1-94; Coverage: 100%)
Gene names: J0526, QCR8, YJL166W
Sequence domains: UcrQ family
Cytochrome b Chains: J, j
Molecule details ›
Chains: J, j
Length: 385 amino acids
Theoretical weight: 43.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00163 (Residues: 1-385; Coverage: 100%)
Gene names: COB, CYTB, Q0105
Sequence domains:
Cytochrome c oxidase subunit 1 Chain: K
Molecule details ›
Chain: K
Length: 534 amino acids
Theoretical weight: 58.83 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00401 (Residues: 1-534; Coverage: 100%)
Gene names: COX1, OXI3, Q0045
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Cytochrome c1, heme protein, mitochondrial Chains: L, l
Molecule details ›
Chains: L, l
Length: 309 amino acids
Theoretical weight: 34.1 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07143 (Residues: 1-309; Coverage: 100%)
Gene names: CTC1, CYT1, YOR065W, YOR29-16
Sequence domains: Cytochrome C1 family
Cytochrome c oxidase subunit 8, mitochondrial Chain: M
Molecule details ›
Chain: M
Length: 78 amino acids
Theoretical weight: 8.92 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04039 (Residues: 1-78; Coverage: 100%)
Gene names: COX8, L8084.14, YLR395C
Sequence domains: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 7, mitochondrial Chain: N
Molecule details ›
Chain: N
Length: 60 amino acids
Theoretical weight: 6.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10174 (Residues: 1-60; Coverage: 100%)
Gene names: COX7, YM9920.10C, YMR256C
Sequence domains: Cytochrome c oxidase subunit VII
Cytochrome c oxidase subunit 3 Chain: O
Molecule details ›
Chain: O
Length: 269 amino acids
Theoretical weight: 30.38 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00420 (Residues: 1-269; Coverage: 100%)
Gene names: COX3, OXI2, Q0275
Sequence domains: Cytochrome c oxidase subunit III
Cytochrome c oxidase subunit 2 Chain: P
Molecule details ›
Chain: P
Length: 251 amino acids
Theoretical weight: 28.59 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00410 (Residues: 1-251; Coverage: 100%)
Gene names: COX2, OXI1, Q0250
Sequence domains:
Cytochrome c oxidase subunit 6, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 148 amino acids
Theoretical weight: 17.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00427 (Residues: 1-148; Coverage: 100%)
Gene names: COX6, YHR051W
Sequence domains: Cytochrome c oxidase subunit Va
Cytochrome c oxidase subunit 9, mitochondrial Chain: R
Molecule details ›
Chain: R
Length: 59 amino acids
Theoretical weight: 6.97 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07255 (Residues: 1-59; Coverage: 100%)
Gene names: COX9, D2520, YDL067C
Cytochrome c oxidase subunit 13, mitochondrial Chain: S
Molecule details ›
Chain: S
Length: 129 amino acids
Theoretical weight: 15.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32799 (Residues: 1-129; Coverage: 100%)
Gene names: COX13, G1341, YGL191W
Sequence domains: Cytochrome c oxidase subunit VIa
Cytochrome c oxidase subunit 4, mitochondrial Chain: T
Molecule details ›
Chain: T
Length: 155 amino acids
Theoretical weight: 17.16 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04037 (Residues: 1-155; Coverage: 100%)
Gene names: COX4, G1362, YGL187C
Sequence domains: Cytochrome c oxidase subunit Vb
Cytochrome c oxidase subunit 12, mitochondrial Chain: U
Molecule details ›
Chain: U
Length: 83 amino acids
Theoretical weight: 9.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01519 (Residues: 1-83; Coverage: 100%)
Gene names: COX12, YLR038C
Sequence domains: Cytochrome oxidase c subunit VIb
Cytochrome c oxidase subunit 26, mitochondrial Chain: V
Molecule details ›
Chain: V
Length: 66 amino acids
Theoretical weight: 7.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q2V2P9 (Residues: 1-66; Coverage: 100%)
Gene names: COX26, YDR119W-A
Cytochrome c oxidase subunit 5A, mitochondrial Chain: W
Molecule details ›
Chain: W
Length: 153 amino acids
Theoretical weight: 17.16 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00424 (Residues: 1-153; Coverage: 100%)
Gene names: COX5A, N2474, YNL052W, YNL2474W
Sequence domains: Cytochrome c oxidase subunit IV

Ligands and Environments

9 bound ligands:
Ligand PEF 15 x PEF
Ligand PGT 7 x PGT
Ligand FES 2 x FES
Ligand PCF 4 x PCF
Ligand HEM 6 x HEM
Ligand UQ6 2 x UQ6
Ligand CU 1 x CU
Ligand HEA 2 x HEA
Ligand CUA 2 x CUA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-28011

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