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CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae

Electron Microscopy
3.17Å resolution
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
Assembly composition:
hetero 32-mer (preferred)
Entry contents: 25 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 32-mer
Accessible surface area: 217879.48 Å2
Buried surface area: 161878.66 Å2
Dissociation area: 1,348.35 Å2
Dissociation energy (ΔGdiss): 8.14 kcal/mol
Dissociation entropy (TΔSdiss): 12.26 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-132269

Macromolecules

Cytochrome c oxidase subunit 1
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
Pfam: Cytochrome C and Quinol oxidase polypeptide I
InterPro:
Cytochrome c oxidase subunit 1 in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 1 in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 1 in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 2
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
Pfam:
InterPro:
Cytochrome c oxidase subunit 2 in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 2 in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 2 in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 3
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
Pfam: Cytochrome c oxidase subunit III
InterPro:
Cytochrome c oxidase subunit 3 in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 3 in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 3 in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 4, mitochondrial
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
Pfam: Cytochrome c oxidase subunit Vb
InterPro:
Cytochrome c oxidase subunit 4, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 4, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 4, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 5A, mitochondrial
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
Pfam: Cytochrome c oxidase subunit IV
InterPro:
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 5A, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 6, mitochondrial
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
Pfam: Cytochrome c oxidase subunit Va
InterPro:
Cytochrome c oxidase subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 7, mitochondrial
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
Pfam: Cytochrome c oxidase subunit VII
InterPro: Cytochrome c oxidase subunit VII
Cytochrome c oxidase subunit 7, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 7, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 7, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 8, mitochondrial
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
Pfam: Cytochrome c oxidase subunit VIIc
InterPro:
Cytochrome c oxidase subunit 8, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 8, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 8, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 9, mitochondrial
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
InterPro: Cytochrome c oxidase, subunit VIIa, fungal
Cytochrome c oxidase subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 12, mitochondrial
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
Pfam: Cytochrome oxidase c subunit VIb
InterPro:
Cytochrome c oxidase subunit 12, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 12, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 12, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 13, mitochondrial
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
Pfam: Cytochrome c oxidase subunit VIa
InterPro:
Cytochrome c oxidase subunit 13, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 13, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 13, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c oxidase subunit 26, mitochondrial
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 c oxidase subunit 26, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c oxidase subunit 26, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c oxidase subunit 26, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 1, mitochondrial
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
Pfam:
InterPro:
Cytochrome b-c1 complex subunit 1, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 1, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 1, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 2, mitochondrial
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
Pfam: Insulinase (Peptidase family M16)
InterPro:
Cytochrome b-c1 complex subunit 2, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 2, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 2, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b
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
Pfam:
InterPro:
Cytochrome b in PDB entry 6ymx, assembly 1, front view.
Cytochrome b in PDB entry 6ymx, assembly 1, side view.
Cytochrome b in PDB entry 6ymx, assembly 1, top view.
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Cytochrome c1, heme protein, mitochondrial
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
Pfam: Cytochrome C1 family
InterPro:
Cytochrome c1, heme protein, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome c1, heme protein, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome c1, heme protein, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit Rieske, mitochondrial
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
Pfam:
InterPro:
Cytochrome b-c1 complex subunit Rieske, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit Rieske, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit Rieske, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 6, mitochondrial
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
Pfam: Ubiquinol-cytochrome C reductase hinge protein
InterPro:
Cytochrome b-c1 complex subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 7, mitochondrial
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
Pfam: Ubiquinol-cytochrome C reductase complex 14kD subunit
InterPro:
Cytochrome b-c1 complex subunit 7, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 7, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 7, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 8, mitochondrial
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
Pfam: UcrQ family
InterPro:
Cytochrome b-c1 complex subunit 8, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 8, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 8, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 9, mitochondrial
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
Pfam: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
InterPro:
Cytochrome b-c1 complex subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 6, mitochondrial
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
Pfam: Ubiquinol-cytochrome C reductase hinge protein
InterPro:
Cytochrome b-c1 complex subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 6, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 9, mitochondrial
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
Pfam: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
InterPro:
Cytochrome b-c1 complex subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 9, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 10, mitochondrial
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
Pfam: Ubiquinol-cytochrome-c reductase complex subunit (QCR10)
InterPro: Cytochrome b-c1 complex subunit 10, fungi
Cytochrome b-c1 complex subunit 10, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 10, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 10, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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Cytochrome b-c1 complex subunit 10, mitochondrial
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
Pfam: Ubiquinol-cytochrome-c reductase complex subunit (QCR10)
InterPro: Cytochrome b-c1 complex subunit 10, fungi
Cytochrome b-c1 complex subunit 10, mitochondrial in PDB entry 6ymx, assembly 1, front view.
Cytochrome b-c1 complex subunit 10, mitochondrial in PDB entry 6ymx, assembly 1, side view.
Cytochrome b-c1 complex subunit 10, mitochondrial in PDB entry 6ymx, assembly 1, top view.
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