2YBB image
Deposition Date 2011-03-02
Release Date 2011-10-19
Last Version Date 2024-11-20
Entry Detail
PDB ID:
2YBB
Keywords:
Title:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
19.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT 1
Gene (Uniprot):nqo1
Chain IDs:A (auth: 1)
Chain Length:438
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT 2
Gene (Uniprot):nqo2
Chain IDs:B (auth: 2)
Chain Length:181
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT 3
Gene (Uniprot):nqo3
Chain IDs:C (auth: 3)
Chain Length:783
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT 4
Gene (Uniprot):nqo4
Chain IDs:D (auth: 4)
Chain Length:409
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT 5
Gene (Uniprot):nqo5
Chain IDs:E (auth: 5)
Chain Length:207
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT 6
Gene (Uniprot):nqo6
Chain IDs:F (auth: 6)
Chain Length:181
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT 15
Gene (Uniprot):nqo15
Chain IDs:G (auth: 7)
Chain Length:129
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT 9
Gene (Uniprot):nqo9
Chain IDs:H (auth: 8)
Chain Length:182
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
Gene (Uniprot):UQCRC1
Chain IDs:I (auth: A), HA (auth: a)
Chain Length:446
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
Gene (Uniprot):UQCRC2
Chain IDs:J (auth: B), IA (auth: b)
Chain Length:439
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B
Gene (Uniprot):MT-CYB
Chain IDs:K (auth: C), JA (auth: c)
Chain Length:379
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
Gene (Uniprot):CYC1
Chain IDs:L (auth: D), KA (auth: d)
Chain Length:241
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
Gene (Uniprot):UQCRFS1
Chain IDs:M (auth: E), LA (auth: e)
Chain Length:196
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT 7
Gene (Uniprot):UQCRB
Mutations:YES
Chain IDs:N (auth: F), MA (auth: f)
Chain Length:110
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT 8
Gene (Uniprot):UQCRQ
Chain IDs:O (auth: G), NA (auth: g)
Chain Length:81
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
Gene (Uniprot):UQCRH
Chain IDs:P (auth: H), OA (auth: h)
Chain Length:78
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
Gene (Uniprot):UQCRFS1
Chain IDs:Q (auth: I), PA (auth: i)
Chain Length:65
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT 9
Gene (Uniprot):UQCR10
Chain IDs:R (auth: J), QA (auth: j)
Chain Length:62
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME B-C1 COMPLEX SUBUNIT 10
Gene (Uniprot):UQCR11
Chain IDs:S (auth: K), RA (auth: k)
Chain Length:56
Number of Molecules:2
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 1
Gene (Uniprot):MT-CO1
Chain IDs:T (auth: L)
Chain Length:514
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 2
Gene (Uniprot):MT-CO2
Chain IDs:U (auth: M)
Chain Length:227
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 3
Gene (Uniprot):MT-CO3
Chain IDs:V (auth: N)
Chain Length:391
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1, MITOCHONDRIAL
Gene (Uniprot):COX4I1
Chain IDs:W (auth: O)
Chain Length:378
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 5A, MITOCHONDRIAL
Gene (Uniprot):COX5A
Chain IDs:X (auth: P)
Chain Length:281
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 5B, MITOCHONDRIAL
Gene (Uniprot):COX5B
Chain IDs:Y (auth: Q)
Chain Length:98
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE POLYPEPTIDE VIA, CYTOCHROME C OXIDASE POLYPEPTIDE VB
Gene (Uniprot):COX6A2
Chain IDs:Z (auth: R)
Chain Length:84
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 6B1
Gene (Uniprot):COX6B1
Chain IDs:AA (auth: S)
Chain Length:85
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 6C
Gene (Uniprot):COX6C
Chain IDs:BA (auth: T)
Chain Length:73
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 7A1, MITOCHONDRIAL
Gene (Uniprot):COX7A1
Chain IDs:CA (auth: U)
Chain Length:59
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 7B, MITOCHONDRIAL
Gene (Uniprot):COX7B
Chain IDs:DA (auth: V)
Chain Length:56
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 7C, MITOCHONDRIAL
Gene (Uniprot):COX7C
Chain IDs:EA (auth: W)
Chain Length:47
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C OXIDASE SUBUNIT 8B, MITOCHONDRIAL
Gene (Uniprot):COX8B
Chain IDs:FA (auth: X)
Chain Length:46
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:CYTOCHROME C
Gene (Uniprot):CYCS
Chain IDs:GA (auth: Y)
Chain Length:104
Number of Molecules:1
Biological Source:BOS TAURUS
Polymer Type:polypeptide(L)
Molecule:NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT L,
Chain IDs:SA (auth: m)
Chain Length:227
Number of Molecules:1
Biological Source:ESCHERICHIA COLI
Polymer Type:polypeptide(L)
Molecule:NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT M,
Chain IDs:TA (auth: n)
Chain Length:391
Number of Molecules:1
Biological Source:ESCHERICHIA COLI
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT N
Chain IDs:UA (auth: o)
Chain Length:378
Number of Molecules:1
Biological Source:ESCHERICHIA COLI
Polymer Type:polypeptide(L)
Molecule:NADH-QUINONE OXIDOREDUCTASE SUBUNIT K
Chain IDs:VA (auth: p)
Chain Length:281
Number of Molecules:1
Biological Source:ESCHERICHIA COLI
Primary Citation
Arrangement of Electron Transport Chain Components in Bovine Mitochondrial Supercomplex I(1)III(2)Iv(1).
Embo J. 30 4652 ? (2011)
PMID: 21909073 DOI: 10.1038/EMBOJ.2011.324

Abstact

The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-Å 3D map of the 1.7-MDa amphipol-solubilized supercomplex I(1)III(2)IV(1) from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X-ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol-binding sites of complexes I and III, and of 10-11 nm between the cytochrome c binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred.

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Primary Citation of related structures