› 2ybb

Electron Microscopy
19Å resolution

Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

Released:
DOI: 10.2210/pdb2ybb/pdb
PDB entry 2ybb coloured by chain, front view.
PDB entry 2ybb coloured by chain, side view.
PDB entry 2ybb coloured by chain, top view.
Source organisms:
Primary publication:
Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1.
Althoff T, Mills DJ, Popot JL, Kühlbrandt W
EMBO J 30 4652-64 (2011)
PMID: 21909073
Related structures: EMD-1876

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 48-mer (preferred)
PDBe Complex ID:
PDB-CPX-132261 (preferred)
Entry contents:
37 distinct polypeptide molecules
Macromolecules (37 distinct):
NADH-quinone oxidoreductase subunit 1 Chain: 1
Molecule details ›
Chain: 1
Length: 438 amino acids
Theoretical weight: 48.69 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56222 (Residues: 1-438; Coverage: 100%)
Gene names: TTHA0089, nqo1
Sequence domains:
NADH-quinone oxidoreductase subunit 2 Chain: 2
Molecule details ›
Chain: 2
Length: 181 amino acids
Theoretical weight: 20.31 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56221 (Residues: 1-181; Coverage: 100%)
Gene names: TTHA0088, nqo2
Sequence domains: Thioredoxin-like [2Fe-2S] ferredoxin
NADH-quinone oxidoreductase subunit 3 Chain: 3
Molecule details ›
Chain: 3
Length: 783 amino acids
Theoretical weight: 86.66 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56223 (Residues: 1-783; Coverage: 100%)
Gene names: TTHA0090, nqo3
Sequence domains:
NADH-quinone oxidoreductase subunit 4 Chain: 4
Molecule details ›
Chain: 4
Length: 409 amino acids
Theoretical weight: 46.43 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56220 (Residues: 1-409; Coverage: 100%)
Gene names: TTHA0087, nqo4
Sequence domains: Respiratory-chain NADH dehydrogenase, 49 Kd subunit
NADH-quinone oxidoreductase subunit 5 Chain: 5
Molecule details ›
Chain: 5
Length: 207 amino acids
Theoretical weight: 23.89 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56219 (Residues: 1-207; Coverage: 100%)
Gene names: TTHA0086, nqo5
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
NADH-quinone oxidoreductase subunit 6 Chain: 6
Molecule details ›
Chain: 6
Length: 181 amino acids
Theoretical weight: 20.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56218 (Residues: 1-181; Coverage: 100%)
Gene names: TTHA0085, nqo6
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
NADH-quinone oxidoreductase subunit 15 Chain: 7
Molecule details ›
Chain: 7
Length: 129 amino acids
Theoretical weight: 14.81 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKZ7 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA0496, nqo15
Sequence domains: NADH-quinone oxidoreductase chain 15
NADH-quinone oxidoreductase subunit 9 Chain: 8
Molecule details ›
Chain: 8
Length: 182 amino acids
Theoretical weight: 20.11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56224 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA0092, nqo9
Sequence domains: 4Fe-4S binding domain
Cytochrome b-c1 complex subunit 1, mitochondrial Chains: A, a
Molecule details ›
Chains: A, a
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, b
Molecule details ›
Chains: B, b
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, c
Molecule details ›
Chains: C, c
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, d
Molecule details ›
Chains: D, d
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, e
Molecule details ›
Chains: E, e
Length: 196 amino acids
Theoretical weight: 21.64 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 79-274; Coverage: 72%)
Gene name: UQCRFS1
Sequence domains:
Cytochrome b-c1 complex subunit 7 Chains: F, f
Molecule details ›
Chains: F, f
Length: 110 amino acids
Theoretical weight: 13.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00129 (Residues: 2-111; Coverage: 99%)
Gene name: UQCRB
Sequence domains: Ubiquinol-cytochrome C reductase complex 14kD subunit
Cytochrome b-c1 complex subunit 8 Chains: G, g
Molecule details ›
Chains: G, g
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, h
Molecule details ›
Chains: H, h
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, i
Molecule details ›
Chains: I, i
Length: 65 amino acids
Theoretical weight: 6.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13272 (Residues: 14-78; Coverage: 24%)
Gene name: UQCRFS1
Sequence domains: Ubiquinol-cytochrome c reductase 8 kDa, N-terminal
Cytochrome b-c1 complex subunit 9 Chains: J, j
Molecule details ›
Chains: J, j
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, k
Molecule details ›
Chains: K, k
Length: 56 amino acids
Theoretical weight: 6.37 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
Cytochrome c oxidase subunit 1 Chain: L
Molecule details ›
Chain: L
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: M
Molecule details ›
Chain: M
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:
Cytochrome c oxidase subunit 3 Chain: N
Molecule details ›
Chain: N
Length: 261 amino acids
Theoretical weight: 29.96 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00415 (Residues: 1-261; Coverage: 100%)
Gene names: COIII, COXIII, MT-CO3, MTCO3
Sequence domains: Cytochrome c oxidase subunit III
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chain: O
Molecule details ›
Chain: O
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: P
Molecule details ›
Chain: P
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: Q
Molecule details ›
Chain: Q
Length: 98 amino acids
Theoretical weight: 10.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00428 (Residues: 32-129; Coverage: 76%)
Gene name: COX5B
Sequence domains: Cytochrome c oxidase subunit Vb
Cytochrome c oxidase subunit 6A2, mitochondrial Chain: R
Molecule details ›
Chain: R
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
Sequence domains: Cytochrome c oxidase subunit VIa
Cytochrome c oxidase subunit 6B1 Chain: S
Molecule details ›
Chain: S
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: T
Molecule details ›
Chain: T
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: U
Molecule details ›
Chain: U
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: V
Molecule details ›
Chain: V
Length: 56 amino acids
Theoretical weight: 6.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13183 (Residues: 25-80; Coverage: 70%)
Gene name: COX7B
Sequence domains: Cytochrome C oxidase chain VIIB
Cytochrome c oxidase subunit 7C, mitochondrial Chain: W
Molecule details ›
Chain: W
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
Sequence domains: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 8B, mitochondrial Chain: X
Molecule details ›
Chain: X
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 Chain: Y
Molecule details ›
Chain: Y
Length: 104 amino acids
Theoretical weight: 11.6 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P62894 (Residues: 2-105; Coverage: 99%)
Gene names: CYC, CYCS
Sequence domains: Cytochrome c
NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT L, Chain: m
Molecule details ›
Chain: m
Length: 474 amino acids
Theoretical weight: 40.36 KDa
Source organism: Escherichia coli BL21
NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT M, Chain: n
Molecule details ›
Chain: n
Length: 391 amino acids
Theoretical weight: 33.29 KDa
Source organism: Escherichia coli BL21
NADH-QUINONE OXIDOREDUCTASE SUBUNIT N Chain: o
Molecule details ›
Chain: o
Length: 378 amino acids
Theoretical weight: 32.19 KDa
Source organism: Escherichia coli BL21
NADH-QUINONE OXIDOREDUCTASE SUBUNIT K Chain: p
Molecule details ›
Chain: p
Length: 281 amino acids
Theoretical weight: 23.93 KDa
Source organism: Escherichia coli BL21

Ligands and Environments


Cofactor: Ligand HEC 2 x HEC

Cofactor: Ligand UQ1 2 x UQ1

Cofactor: Ligand HEM 5 x HEM

Cofactor: Ligand HEA 2 x HEA
10 bound ligands:
Ligand SF4 7 x SF4
Ligand FMN 1 x FMN
Ligand NAI 1 x NAI
Ligand MG 7 x MG
Ligand FES 4 x FES
Ligand CA 1 x CA
Ligand SMA 2 x SMA
Ligand CDL 4 x CDL
Ligand CU 3 x CU
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 19Å
Relevant EMDB volumes: EMD-1876

Quick links

Citations

67 review citations

OXPHOS mutations and neurodegeneration.
Koopman et al. (2013)
66 more

15 mentions without citation

Cardiolipin-dependent formation of mitochondrial respiratory supercomplexes.
Mileykovskaya et al. (2014)
14 more