PDBe 5gpn

Electron Microscopy
5.4Å resolution

Architecture of mammalian respirasome

Released:
Source organisms:
Primary publication:
The architecture of the mammalian respirasome.
Nature 537 639-43 (2016)
PMID: 27654917
Related structures: EMD-9534

Function and Biology Details

Reactions catalysed:
Quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H(+)
NADH + ubiquinone + 5 H(+)(In) = NAD(+) + ubiquinol + 4 H(+)(Out)
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 84-mer (preferred)
Entry contents:
63 distinct polypeptide molecules
Macromolecules (63 distinct):
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: A, M
Molecule details ›
Chains: A, M
Length: 446 amino acids
Theoretical weight: 49.27 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P31800 (Residues: 35-480; Coverage: 93%)
Gene name: UQCRC1
Sequence domains:
Cytochrome b-c1 complex subunit 2, mitochondrial Chains: B, N
Molecule details ›
Chains: B, N
Length: 439 amino acids
Theoretical weight: 46.58 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P23004 (Residues: 15-453; Coverage: 97%)
Gene name: UQCRC2
Sequence domains:
Cytochrome b Chains: C, O
Molecule details ›
Chains: C, O
Length: 379 amino acids
Theoretical weight: 42.62 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00157 (Residues: 1-379; Coverage: 100%)
Gene names: COB, CYTB, MT-CYB, MTCYB
Sequence domains:
Cytochrome c1, heme protein, mitochondrial Chains: D, P
Molecule details ›
Chains: D, P
Length: 241 amino acids
Theoretical weight: 27.32 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00125 (Residues: 85-325; Coverage: 74%)
Gene name: CYC1
Sequence domains: Cytochrome C1 family
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: E, Q
Molecule details ›
Chains: E, Q
Length: 274 amino acids
Theoretical weight: 29.57 KDa
Source organism: Bos taurus
Cytochrome b-c1 complex subunit 7 Chains: F, R
Molecule details ›
Chains: F, R
Length: 110 amino acids
Theoretical weight: 13.37 KDa
Source organism: Bos taurus
Cytochrome b-c1 complex subunit 8 Chains: G, S
Molecule details ›
Chains: G, S
Length: 81 amino acids
Theoretical weight: 9.61 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13271 (Residues: 2-82; Coverage: 99%)
Gene name: UQCRQ
Sequence domains: UcrQ family
Cytochrome b-c1 complex subunit 6, mitochondrial Chains: H, T
Molecule details ›
Chains: H, T
Length: 78 amino acids
Theoretical weight: 9.19 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00126 (Residues: 14-91; Coverage: 86%)
Gene name: UQCRH
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Cytochrome b-c1 complex subunit 9 Chains: I, U
Molecule details ›
Chains: I, U
Length: 78 amino acids
Theoretical weight: 7.96 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 1-78; Coverage: 29%)
Gene name: UQCRFS1
Sequence domains: Ubiquinol-cytochrome c reductase 8 kDa, N-terminal
Cytochrome b-c1 complex subunit 9 Chains: J, L
Molecule details ›
Chains: J, L
Length: 62 amino acids
Theoretical weight: 7.21 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00130 (Residues: 2-63; Coverage: 97%)
Gene name: UQCR10
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Cytochrome b-c1 complex subunit 10 Chains: K, V
Molecule details ›
Chains: K, V
Length: 56 amino acids
Theoretical weight: 6.53 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07552 (Residues: 1-56; Coverage: 100%)
Gene names: UQCR, UQCR11
Sequence domains: Ubiquinol-cytochrome C reductase complex, 6.4kD protein
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 Chain: W
Molecule details ›
Chain: W
Length: 264 amino acids
Theoretical weight: 30.24 KDa
Source organism: Sus scrofa
NADH:ubiquinone oxidoreductase core subunit S1 Chain: Y
Molecule details ›
Chain: Y
Length: 727 amino acids
Theoretical weight: 79.63 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SHD7 (Residues: 1-611; Coverage: 100%)
Gene name: NDUFS1
Sequence domains:
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 Chain: Z
Molecule details ›
Chain: Z
Length: 463 amino acids
Theoretical weight: 52.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S1A8 (Residues: 11-473; Coverage: 100%)
Gene name: NDUFS2
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7 Chain: a
Molecule details ›
Chain: a
Length: 216 amino acids
Theoretical weight: 23.78 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LK43 (Residues: 1-21, 22-196; Coverage: 100%)
Gene name: NDUFS7
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 Chain: b
Molecule details ›
Chain: b
Length: 212 amino acids
Theoretical weight: 23.89 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 464 amino acids
Theoretical weight: 50.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RVN1 (Residues: 1-464; Coverage: 100%)
Gene name: NDUFV1
Sequence domains:
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: d
Molecule details ›
Chain: d
Length: 249 amino acids
Theoretical weight: 27.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SM98 (Residues: 1-220; Coverage: 98%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH-ubiquinone oxidoreductase chain 1 Chain: e
Molecule details ›
Chain: e
Length: 318 amino acids
Theoretical weight: 35.67 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79874 (Residues: 1-318; Coverage: 100%)
Gene names: MT-ND1, MTND1, NADH1, ND1
Sequence domains: NADH dehydrogenase
NADH-ubiquinone oxidoreductase chain 2 Chain: f
Molecule details ›
Chain: f
Length: 347 amino acids
Theoretical weight: 39.08 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79875 (Residues: 1-347; Coverage: 100%)
Gene names: MT-ND2, MTND2, NADH2, ND2
Sequence domains:
NADH-ubiquinone oxidoreductase chain 3 Chain: g
Molecule details ›
Chain: g
Length: 115 amino acids
Theoretical weight: 13 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79880 (Residues: 1-115; Coverage: 100%)
Gene names: MT-ND3, MTND3, NADH3, ND3
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
NADH-ubiquinone oxidoreductase chain 4 Chain: h
Molecule details ›
Chain: h
Length: 459 amino acids
Theoretical weight: 51.86 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79881 (Residues: 1-459; Coverage: 100%)
Gene names: MT-ND4, MTND4, NADH4, ND4
Sequence domains:
NADH-ubiquinone oxidoreductase chain 4L Chain: i
Molecule details ›
Chain: i
Length: 98 amino acids
Theoretical weight: 10.83 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P56632 (Residues: 1-98; Coverage: 100%)
Gene names: MT-ND4L, MTND4L, NADH4L, ND4L
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
NADH-ubiquinone oxidoreductase chain 5 Chain: j
Molecule details ›
Chain: j
Length: 606 amino acids
Theoretical weight: 68.7 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q9TDR1 (Residues: 1-606; Coverage: 100%)
Gene names: MT-ND5, MTND5, NADH5, ND5
Sequence domains:
NADH-ubiquinone oxidoreductase chain 6 Chains: k, l
Molecule details ›
Chains: k, l
Length: 175 amino acids
Theoretical weight: 19.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: O79882 (Residues: 1-175; Coverage: 100%)
Gene names: MT-ND6, MTND6, NADH6, ND6
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 6
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 Chain: m
Molecule details ›
Chain: m
Length: 84 amino acids
Theoretical weight: 9.23 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RNI5 (Residues: 1-84; Coverage: 100%)
Gene name: NDUFA3
Sequence domains: NADH dehydrogenase 1 alpha subcomplex subunit 3
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Chain: n
Molecule details ›
Chain: n
Length: 99 amino acids
Theoretical weight: 11.1 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: o
Molecule details ›
Chain: o
Length: 106 amino acids
Theoretical weight: 12.51 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SV23 (Residues: 1-106; Coverage: 100%)
Gene name: NDUFS5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9 Chain: p
Molecule details ›
Chain: p
Length: 377 amino acids
Theoretical weight: 42.61 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SL07 (Residues: 1-377; Coverage: 100%)
Gene name: NDUFA9
Sequence domains: NmrA-like family
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial Chains: q, v
Molecule details ›
Chains: q, v
Length: 357 amino acids
Theoretical weight: 40.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SIS9 (Residues: 1-357; Coverage: 100%)
Gene name: NDUFA10
Sequence domains: Deoxynucleoside kinase
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 Chain: r
Molecule details ›
Chain: r
Length: 144 amino acids
Theoretical weight: 16.91 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S6Q1 (Residues: 16-159; Coverage: 91%)
Gene name: NDUFA13
Sequence domains: GRIM-19 protein
Acyl carrier protein Chains: Aa, t
Molecule details ›
Chains: Aa, t
Length: 156 amino acids
Theoretical weight: 17.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SAB6 (Residues: 1-156; Coverage: 100%)
Gene name: NDUFAB1
Sequence domains: Phosphopantetheine attachment site
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5 Chains: Ai, u
Molecule details ›
Chains: Ai, u
Length: 189 amino acids
Theoretical weight: 21.59 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SGC6 (Residues: 1-189; Coverage: 100%)
Gene name: NDUFB5
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit
Mitochondrial NADH dehydrogenase Fe-S protein 4 Chain: w
Molecule details ›
Chain: w
Length: 175 amino acids
Theoretical weight: 19.72 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: G8IFA6 (Residues: 1-175; Coverage: 100%)
Sequence domains: ETC complex I subunit conserved region
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: x
Molecule details ›
Chain: x
Length: 123 amino acids
Theoretical weight: 13.35 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S031 (Residues: 1-123; Coverage: 100%)
Gene name: NDUFS6
Sequence domains: Zinc-finger domain
Cytochrome c oxidase subunit 3 Chain: 0
Molecule details ›
Chain: 0
Length: 261 amino acids
Theoretical weight: 29.94 KDa
Source organism: Bos taurus
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chain: 1
Molecule details ›
Chain: 1
Length: 147 amino acids
Theoretical weight: 17.18 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00423 (Residues: 23-169; Coverage: 87%)
Gene names: COX4, COX4I1
Sequence domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 5A, mitochondrial Chain: 2
Molecule details ›
Chain: 2
Length: 109 amino acids
Theoretical weight: 12.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00426 (Residues: 44-152; Coverage: 72%)
Gene name: COX5A
Sequence domains: Cytochrome c oxidase subunit Va
Cytochrome c oxidase subunit 5B, mitochondrial Chain: 3
Molecule details ›
Chain: 3
Length: 98 amino acids
Theoretical weight: 10.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00428 (Residues: 32-129; Coverage: 76%)
Gene name: COX5B
Cytochrome c oxidase subunit 6A2, mitochondrial Chain: 4
Molecule details ›
Chain: 4
Length: 84 amino acids
Theoretical weight: 9.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07471 (Residues: 13-96; Coverage: 87%)
Gene names: COX6A, COX6A2
Cytochrome c oxidase subunit 6B1 Chain: 5
Molecule details ›
Chain: 5
Length: 85 amino acids
Theoretical weight: 10.04 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00429 (Residues: 2-86; Coverage: 99%)
Gene names: COX6B, COX6B1
Sequence domains: Cytochrome oxidase c subunit VIb
Cytochrome c oxidase subunit 6C Chain: 6
Molecule details ›
Chain: 6
Length: 73 amino acids
Theoretical weight: 8.49 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P04038 (Residues: 2-74; Coverage: 99%)
Gene name: COX6C
Sequence domains: Cytochrome c oxidase subunit VIc
Cytochrome c oxidase subunit 7A1, mitochondrial Chain: 7
Molecule details ›
Chain: 7
Length: 59 amino acids
Theoretical weight: 6.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07470 (Residues: 22-80; Coverage: 74%)
Gene names: COX7A, COX7A1, COX7AH
Sequence domains: Cytochrome c oxidase subunit VII
Cytochrome c oxidase subunit 7B, mitochondrial Chain: 8
Molecule details ›
Chain: 8
Length: 56 amino acids
Theoretical weight: 6.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13183 (Residues: 25-80; Coverage: 70%)
Gene name: COX7B
Cytochrome c oxidase subunit 7C, mitochondrial Chain: 9
Molecule details ›
Chain: 9
Length: 47 amino acids
Theoretical weight: 5.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00430 (Residues: 17-63; Coverage: 75%)
Gene names: COX7C, COX7CP1
Cytochrome c oxidase subunit 8B, mitochondrial Chain: s
Molecule details ›
Chain: s
Length: 46 amino acids
Theoretical weight: 4.97 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P10175 (Residues: 25-70; Coverage: 66%)
Gene names: COX8B, COX8H
Sequence domains: Cytochrome oxidase c subunit VIII
Cytochrome c oxidase subunit 1 Chain: y
Molecule details ›
Chain: y
Length: 514 amino acids
Theoretical weight: 57.07 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00396 (Residues: 1-514; Coverage: 100%)
Gene names: COI, COXI, MT-CO1, MTCO1
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Cytochrome c oxidase subunit 2 Chain: z
Molecule details ›
Chain: z
Length: 227 amino acids
Theoretical weight: 26.04 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P68530 (Residues: 1-227; Coverage: 100%)
Gene names: COII, COX2, COXII, MT-CO2, MTCO2
Sequence domains:
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment Chains: Ab, Ah
Molecule details ›
Chains: Ab, Ah
Length: 134 amino acids
Theoretical weight: 11.42 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: Ac
Molecule details ›
Chain: Ac
Length: 70 amino acids
Theoretical weight: 8.09 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GR43 (Residues: 1-70; Coverage: 100%)
Gene name: NDUFA1
Sequence domains: NADH-ubiquinone oxidoreductase MWFE subunit
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment Chains: Ad, Ao, Ap, Av
Molecule details ›
Chains: Ad, Ao, Ap, Av
Length: 43 amino acids
Theoretical weight: 3.68 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: Ae
Molecule details ›
Chain: Ae
Length: 116 amino acids
Theoretical weight: 13.32 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: Af
Molecule details ›
Chain: Af
Length: 128 amino acids
Theoretical weight: 14.95 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 Chain: Ag
Molecule details ›
Chain: Ag
Length: 141 amino acids
Theoretical weight: 14.69 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGM4 (Residues: 1-141; Coverage: 100%)
Gene name: NDUFA11
Sequence domains: Tim17/Tim22/Tim23/Pmp24 family
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: Aj
Molecule details ›
Chain: Aj
Length: 176 amino acids
Theoretical weight: 20.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LDC3 (Residues: 1-176; Coverage: 100%)
Gene name: NDUFB10
Sequence domains: NADH-ubiquinone oxidoreductase subunit 10
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: Ak
Molecule details ›
Chain: Ak
Length: 178 amino acids
Theoretical weight: 21.73 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GSE5 (Residues: 1-178; Coverage: 99%)
Gene name: NDUFB9
Sequence domains: Complex 1 protein (LYR family)
NADH dehydrogenase [ubiquinone] 1 subunit C2 Chain: Al
Molecule details ›
Chain: Al
Length: 122 amino acids
Theoretical weight: 14.33 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 subunit C1 Chain: Am
Molecule details ›
Chain: Am
Length: 76 amino acids
Theoretical weight: 8.63 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RRC9 (Residues: 1-7, 8-16, 17-55; Coverage: 25%)
Gene name: MGARP
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: An
Molecule details ›
Chain: An
Length: 172 amino acids
Theoretical weight: 20.06 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SLR1 (Residues: 78-249; Coverage: 69%)
Gene name: NDUFA8
Sequence domains: CHCH domain
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment Chains: Aq, As, Aw
Molecule details ›
Chains: Aq, As, Aw
Length: 76 amino acids
Theoretical weight: 6.49 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment Chain: Ar
Molecule details ›
Chain: Ar
Length: 34 amino acids
Theoretical weight: 2.91 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment Chain: At
Molecule details ›
Chain: At
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment Chain: Au
Molecule details ›
Chain: Au
Length: 13 amino acids
Theoretical weight: 1.12 KDa
Source organism: Sus scrofa

Ligands and Environments


Cofactor: Ligand HEM 4 x HEM

Cofactor: Ligand HEC 2 x HEC

Cofactor: Ligand NDP 1 x NDP

Cofactor: Ligand HEA 2 x HEA

Cofactor: Ligand FMN 1 x FMN

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.4Å
Relevant EMDB volumes: EMD-9534