PDBe 5gup

Electron Microscopy
4Å resolution

Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1

Released:
Source organism: Sus scrofa
Primary publication:
Structure of Mammalian Respiratory Supercomplex I1III2IV1.
Cell 167 1598-1609.e10 (2016)
PMID: 27912063
Related structures: EMD-9539

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 80-mer (preferred)
Entry contents:
67 distinct polypeptide molecules
Macromolecules (67 distinct):
Cytochrome c oxidase subunit 6C Chain: A
Molecule details ›
Chain: A
Length: 73 amino acids
Theoretical weight: 8.49 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Chain: B
Molecule details ›
Chain: B
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] iron-sulfur protein 2, mitochondrial Chain: C
Molecule details ›
Chain: C
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 3, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 264 amino acids
Theoretical weight: 30.24 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Chain: E
Molecule details ›
Chain: E
Length: 249 amino acids
Theoretical weight: 26.3 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SM98 (Residues: 48-220; Coverage: 77%)
Gene name: NDUFV2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Chain: F
Molecule details ›
Chain: F
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
NADH:ubiquinone oxidoreductase core subunit S1 Chain: G
Molecule details ›
Chain: G
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 8, mitochondrial Chain: H
Molecule details ›
Chain: H
Length: 212 amino acids
Theoretical weight: 23.89 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Chain: I
Molecule details ›
Chain: I
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
Mitochondrial NADH dehydrogenase Fe-S protein 4 Chain: J
Molecule details ›
Chain: J
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] 1 alpha subcomplex subunit 12 Chains: K, R
Molecule details ›
Chains: K, R
Length: 145 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SQP4 (Residues: 1-145; Coverage: 100%)
Gene name: NDUFA12
Sequence domains: NADH ubiquinone oxidoreductase subunit NDUFA12
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial Chain: L
Molecule details ›
Chain: L
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 7 Chain: M
Molecule details ›
Chain: M
Length: 113 amino acids
Theoretical weight: 12.65 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SA62 (Residues: 1-113; Coverage: 100%)
Gene name: NDUFA7
Sequence domains: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Chain: N
Molecule details ›
Chain: N
Length: 116 amino acids
Theoretical weight: 13.32 KDa
Source organism: Sus scrofa
Acyl carrier protein Chains: O, X
Molecule details ›
Chains: O, X
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 alpha subcomplex subunit 2 Chain: P
Molecule details ›
Chain: P
Length: 99 amino acids
Theoretical weight: 11.1 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RGE3 (Residues: 1-99; Coverage: 100%)
Gene name: NDUFA2
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Chain: Q
Molecule details ›
Chain: Q
Length: 128 amino acids
Theoretical weight: 14.95 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Chain: S
Molecule details ›
Chain: S
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 alpha subcomplex subunit 3 Chain: T
Molecule details ›
Chain: T
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 10, mitochondrial Chain: U
Molecule details ›
Chain: U
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 11 Chain: V
Molecule details ›
Chain: V
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 alpha subcomplex subunit 13 Chain: W
Molecule details ›
Chain: W
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
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial Chain: Y
Molecule details ›
Chain: Y
Length: 105 amino acids
Theoretical weight: 11.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SRQ0 (Residues: 1-105; Coverage: 100%)
Gene name: NDUFB2
Sequence domains: NADH dehydrogenase 1 beta subcomplex subunit 2
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 Chain: Z
Molecule details ›
Chain: Z
Length: 98 amino acids
Theoretical weight: 11.13 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SI50 (Residues: 1-98; Coverage: 100%)
Gene name: NDUFB3
Sequence domains: NADH-ubiquinone oxidoreductase B12 subunit family
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial Chain: a
Molecule details ›
Chain: a
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
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 Chain: b
Molecule details ›
Chain: b
Length: 128 amino acids
Theoretical weight: 15.6 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q2EN80 (Residues: 1-128; Coverage: 100%)
Gene name: NDUFB6
Sequence domains: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 186 amino acids
Theoretical weight: 21.7 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RWL7 (Residues: 1-186; Coverage: 100%)
Gene name: NDUFB8
Sequence domains: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 Chain: d
Molecule details ›
Chain: d
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 11, mitochondrial Chain: e
Molecule details ›
Chain: e
Length: 154 amino acids
Theoretical weight: 17.38 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial Chain: f
Molecule details ›
Chain: f
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 subunit C2 Chain: g
Molecule details ›
Chain: g
Length: 122 amino acids
Theoretical weight: 14.33 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 Chain: h
Molecule details ›
Chain: h
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-ubiquinone oxidoreductase chain 2 Chain: i
Molecule details ›
Chain: i
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: j
Molecule details ›
Chain: j
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 4L Chain: k
Molecule details ›
Chain: k
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: l
Molecule details ›
Chain: l
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 Chain: m
Molecule details ›
Chain: m
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 beta subcomplex subunit 1 Chain: n
Molecule details ›
Chain: n
Length: 58 amino acids
Theoretical weight: 7.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SD73 (Residues: 1-58; Coverage: 100%)
Gene name: NDUFB1
Sequence domains: MNLL subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 Chain: o
Molecule details ›
Chain: o
Length: 129 amino acids
Theoretical weight: 15.12 KDa
Source organism: Sus scrofa
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 Chain: p
Molecule details ›
Chain: p
Length: 179 amino acids
Theoretical weight: 21.86 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GSE5 (Residues: 1-179; Coverage: 100%)
Gene name: NDUFB9
Sequence domains: Complex 1 protein (LYR family)
NADH-ubiquinone oxidoreductase chain 4 Chain: q
Molecule details ›
Chain: q
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 1 Chain: r
Molecule details ›
Chain: r
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 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 Chain: s
Molecule details ›
Chain: s
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 beta subcomplex subunit 7 Chain: t
Molecule details ›
Chain: t
Length: 137 amino acids
Theoretical weight: 16.49 KDa
Source organism: Sus scrofa
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: 5, u
Molecule details ›
Chains: 5, u
Length: 480 amino acids
Theoretical weight: 52.76 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SKM0 (Residues: 1-283, 284-459; Coverage: 100%)
Gene name: UQCRC1
Sequence domains:
Cytochrome b-c1 complex subunit 2, mitochondrial Chains: 6, v
Molecule details ›
Chains: 6, v
Length: 453 amino acids
Theoretical weight: 48.26 KDa
Source organism: Sus scrofa
Cytochrome b Chains: 7, w
Molecule details ›
Chains: 7, w
Length: 379 amino acids
Theoretical weight: 42.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q1HBG9 (Residues: 1-379; Coverage: 100%)
Gene names: CYTB, CytB, cytb
Sequence domains:
Cytochrome c1, heme protein, mitochondrial Chains: 8, x
Molecule details ›
Chains: 8, x
Length: 326 amino acids
Theoretical weight: 35.49 KDa
Source organism: Sus scrofa
Cytochrome b-c1 complex subunit 7 Chains: 9, y
Molecule details ›
Chains: 9, y
Length: 111 amino acids
Theoretical weight: 13.59 KDa
Source organism: Sus scrofa
Ubiquinol-cytochrome c reductase complex III subunit VII Chains: Aa, z
Molecule details ›
Chains: Aa, z
Length: 82 amino acids
Theoretical weight: 9.78 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RI18 (Residues: 1-82; Coverage: 100%)
Gene name: UQCRQ
Sequence domains: UcrQ family
Cytochrome b-c1 complex subunit 6 Chains: 0, Ab
Molecule details ›
Chains: 0, Ab
Length: 91 amino acids
Theoretical weight: 10.69 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S3W0 (Residues: 1-91; Coverage: 100%)
Gene name: LOC100524873
Sequence domains: Ubiquinol-cytochrome C reductase hinge protein
Ubiquinol-cytochrome c reductase complex Chains: 1, Ac
Molecule details ›
Chains: 1, Ac
Length: 64 amino acids
Theoretical weight: 7.41 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q2EN79 (Residues: 1-64; Coverage: 100%)
Gene name: UQCR10
Sequence domains: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: 2, 4
Molecule details ›
Chains: 2, 4
Length: 274 amino acids
Theoretical weight: 29.49 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RNZ1 (Residues: 1-274; Coverage: 100%)
Gene name: LOC100522678
Sequence domains:
Cytochrome b-c1 complex subunit 10 Chains: 3, Ad
Molecule details ›
Chains: 3, Ad
Length: 56 amino acids
Theoretical weight: 6.56 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SDI2 (Residues: 1-56; Coverage: 100%)
Gene name: LOC100524239
Sequence domains: Ubiquinol-cytochrome C reductase complex, 6.4kD protein
Cytochrome b-c1 complex subunit Rieske, mitochondrial Chains: Ae, Af
Molecule details ›
Chains: Ae, Af
Length: 78 amino acids
Theoretical weight: 7.9 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RNZ1 (Residues: 1-78; Coverage: 29%)
Gene name: LOC100522678
Sequence domains: Ubiquinol-cytochrome c reductase 8 kDa, N-terminal
Cytochrome c oxidase subunit 8B, mitochondrial Chain: Ag
Molecule details ›
Chain: Ag
Length: 46 amino acids
Theoretical weight: 4.97 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 7A1, mitochondrial Chain: Ah
Molecule details ›
Chain: Ah
Length: 59 amino acids
Theoretical weight: 6.68 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 7B, mitochondrial Chain: Ai
Molecule details ›
Chain: Ai
Length: 56 amino acids
Theoretical weight: 6.37 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 7C, mitochondrial Chain: Aj
Molecule details ›
Chain: Aj
Length: 47 amino acids
Theoretical weight: 5.45 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 1 Chain: Ak
Molecule details ›
Chain: Ak
Length: 514 amino acids
Theoretical weight: 57.07 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 2 Chain: Al
Molecule details ›
Chain: Al
Length: 227 amino acids
Theoretical weight: 26.04 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 3 Chain: Am
Molecule details ›
Chain: Am
Length: 261 amino acids
Theoretical weight: 29.94 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chain: An
Molecule details ›
Chain: An
Length: 147 amino acids
Theoretical weight: 17.18 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 5A Chain: Ao
Molecule details ›
Chain: Ao
Length: 109 amino acids
Theoretical weight: 12.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SJ34 (Residues: 44-152; Coverage: 72%)
Gene name: COX5A
Sequence domains: Cytochrome c oxidase subunit Va
Cytochrome c oxidase subunit 5B, mitochondrial Chain: Ap
Molecule details ›
Chain: Ap
Length: 98 amino acids
Theoretical weight: 10.68 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 6A, mitochondrial Chain: Aq
Molecule details ›
Chain: Aq
Length: 84 amino acids
Theoretical weight: 9.45 KDa
Source organism: Sus scrofa
Cytochrome c oxidase subunit 6B1 Chain: Ar
Molecule details ›
Chain: Ar
Length: 85 amino acids
Theoretical weight: 10.04 KDa
Source organism: Sus scrofa

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
Resolution:
Relevant EMDB volumes: EMD-9539