7DGS image
Deposition Date 2020-11-12
Release Date 2022-05-18
Last Version Date 2022-05-18
Entry Detail
PDB ID:
7DGS
Keywords:
Title:
Activity optimized supercomplex state3
Biological Source:
Source Organism:
Bos taurus (Taxon ID: 9913)
Method Details:
Experimental Method:
Resolution:
7.80 Å
Aggregation State:
TISSUE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 1
Gene (Uniprot):MT-ND1
Chain IDs:H (auth: 1)
Chain Length:318
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 2
Gene (Uniprot):MT-ND2
Chain IDs:D (auth: 2)
Chain Length:347
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 3
Gene (Uniprot):MT-ND3
Chain IDs:I (auth: 3)
Chain Length:115
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4
Gene (Uniprot):MT-ND4
Chain IDs:E (auth: 4)
Chain Length:459
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4L
Gene (Uniprot):MT-ND4L
Chain IDs:F (auth: 5)
Chain Length:98
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 5
Gene (Uniprot):MT-ND5
Chain IDs:C (auth: 6)
Chain Length:606
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 6
Gene (Uniprot):MT-ND6
Chain IDs:B (auth: 7)
Chain Length:175
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Gene (Uniprot):NDUFV1
Chain IDs:G (auth: 8)
Chain Length:444
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Gene (Uniprot):NDUFV2
Chain IDs:A (auth: 9)
Chain Length:217
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
Gene (Uniprot):NDUFS1
Chain IDs:J (auth: A)
Chain Length:704
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6A2, mitochondrial
Gene (Uniprot):COX6A2
Chain IDs:VB (auth: A4)
Chain Length:97
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6B1
Gene (Uniprot):COX6B1
Chain IDs:WB (auth: A5)
Chain Length:86
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 5A, mitochondrial
Gene (Uniprot):COX5A
Chain IDs:TB (auth: A6)
Chain Length:152
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:SB (auth: A7)
Chain Length:169
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 8B, mitochondrial
Gene (Uniprot):COX8B
Chain IDs:BC (auth: A8)
Chain Length:70
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 1
Gene (Uniprot):MT-CO1
Chain IDs:PB (auth: A9)
Chain Length:514
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
Gene (Uniprot):NDUFS2
Chain IDs:K (auth: B)
Chain Length:143
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7B, mitochondrial
Gene (Uniprot):COX7B
Chain IDs:ZB (auth: B0)
Chain Length:80
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7C, mitochondrial
Gene (Uniprot):COX7C
Chain IDs:AC (auth: B1)
Chain Length:63
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 5B, mitochondrial
Gene (Uniprot):COX5B
Chain IDs:UB (auth: B2)
Chain Length:129
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6C
Gene (Uniprot):COX6C
Chain IDs:XB (auth: B6)
Chain Length:74
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 3
Gene (Uniprot):MT-CO3
Chain IDs:RB (auth: B7)
Chain Length:261
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7A1, mitochondrial
Gene (Uniprot):COX7A1
Chain IDs:YB (auth: B8)
Chain Length:80
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 2
Gene (Uniprot):MT-CO2
Chain IDs:QB (auth: B9)
Chain Length:227
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Gene (Uniprot):NDUFS3
Chain IDs:L (auth: C)
Chain Length:127
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Gene (Uniprot):NDUFS7
Chain IDs:M (auth: D)
Chain Length:117
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
Gene (Uniprot):NDUFS8
Chain IDs:N (auth: E)
Chain Length:158
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
Gene (Uniprot):NDUFV3
Chain IDs:O (auth: F)
Chain Length:178
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Gene (Uniprot):NDUFS4
Chain IDs:P (auth: G)
Chain Length:176
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
Gene (Uniprot):NDUFS5
Chain IDs:Q (auth: H)
Chain Length:125
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Gene (Uniprot):NDUFS6
Chain IDs:R (auth: I)
Chain Length:49
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Gene (Uniprot):NDUFA1
Chain IDs:S (auth: J)
Chain Length:120
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Gene (Uniprot):NDUFA2
Chain IDs:T (auth: K)
Chain Length:480
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
Gene (Uniprot):NDUFA3
Chain IDs:U (auth: L)
Chain Length:83
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Gene (Uniprot):NDUFA5
Chain IDs:V (auth: N)
Chain Length:115
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Gene (Uniprot):NDUFA6
Chain IDs:W (auth: O)
Chain Length:127
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
Gene (Uniprot):NDUFA7
Chain IDs:X (auth: P)
Chain Length:196
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Gene (Uniprot):NDUFA8
Chain IDs:Y (auth: Q)
Chain Length:111
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Gene (Uniprot):NDUFA9
Chain IDs:Z (auth: R)
Chain Length:345
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Gene (Uniprot):NDUFA10
Chain IDs:AA (auth: S)
Chain Length:320
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Gene (Uniprot):NDUFA11
Chain IDs:BA (auth: T)
Chain Length:56
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Gene (Uniprot):NDUFA12
Chain IDs:CA (auth: U)
Chain Length:145
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Gene (Uniprot):NDUFA13
Chain IDs:DA (auth: V)
Chain Length:78
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitochondrial
Gene (Uniprot):NDUFAB1
Chain IDs:EA (auth: W), SA (auth: M)
Chain Length:88
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
Gene (Uniprot):NDUFB1
Chain IDs:FA (auth: X)
Chain Length:453
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
Gene (Uniprot):NDUFB2
Chain IDs:GA (auth: Y)
Chain Length:379
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
Gene (Uniprot):NDUFB3
Chain IDs:HA (auth: Z)
Chain Length:325
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
Gene (Uniprot):NDUFB4
Chain IDs:IA (auth: a)
Chain Length:704
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Gene (Uniprot):NDUFB5
Chain IDs:JA (auth: b)
Chain Length:143
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Gene (Uniprot):NDUFB6
Chain IDs:KA (auth: c)
Chain Length:127
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
Gene (Uniprot):NDUFB7
Chain IDs:LA (auth: d)
Chain Length:117
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Gene (Uniprot):NDUFB8
Chain IDs:RA (auth: e)
Chain Length:158
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Gene (Uniprot):NDUFB9
Chain IDs:MA (auth: f)
Chain Length:178
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Gene (Uniprot):NDUFB10
Chain IDs:QA (auth: g)
Chain Length:176
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
Gene (Uniprot):NDUFB11
Chain IDs:NA (auth: h)
Chain Length:125
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Gene (Uniprot):NDUFC1
Chain IDs:OA (auth: i)
Chain Length:49
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 subunit C2
Gene (Uniprot):NDUFC2
Chain IDs:PA (auth: j)
Chain Length:120
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 1, mitochondrial
Gene (Uniprot):UQCRC1
Chain IDs:TA (auth: k), EB (auth: w)
Chain Length:480
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:UA (auth: l), FB (auth: x)
Chain Length:83
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b
Gene (Uniprot):MT-CYB
Chain IDs:VA (auth: m), GB (auth: y)
Chain Length:88
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c1, heme protein, mitochondrial
Gene (Uniprot):CYC1
Chain IDs:WA (auth: o), HB (auth: z)
Chain Length:127
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:XA (auth: p), IB (auth: A0)
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
Chain IDs:YA (auth: q), JB (auth: A1)
Chain Length:111
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 8
Gene (Uniprot):UQCRQ
Chain IDs:ZA (auth: r), KB (auth: A2)
Chain Length:82
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:AB (auth: s), LB (auth: B5)
Chain Length:91
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 10
Gene (Uniprot):UQCR11
Chain IDs:BB (auth: t), MB (auth: A3)
Chain Length:56
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subunit 9
Gene (Uniprot):UQCR10
Chain IDs:CB (auth: u), NB (auth: B4)
Chain Length:64
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:DB (auth: v), OB (auth: B3)
Chain Length:78
Number of Molecules:2
Biological Source:Bos taurus
Primary Citation
A Dynamic Substrate Pool Revealed by cryo-EM of a Lipid-Preserved Respiratory Supercomplex.
Antioxid.Redox Signal. ? ? ? (2022)
PMID: 34913730 DOI: 10.1089/ars.2021.0114

Abstact

Aims: Mitochondrial respiratory supercomplexes mediate redox electron transfer, generating a proton gradient for ATP synthesis. To provide structural information on the function of supercomplexes in physiologically relevant conditions, we conducted cryoelectron microscopy studies with supercomplexes in a lipid-preserving state. Results: Here, we present cryoelectron microscopy structures of bovine respiratory supercomplex I1III2IV1 by using a lipid-preserving sample preparation. The preparation greatly enhances the intercomplex quinone transfer activity. The structures reveal large intercomplex motions that result in different shapes and sizes of the intercomplex space between complexes I and III, forming a dynamic substrate pool. Biochemical and structural analyses indicated that intercomplex phospholipids mediate the intercomplex motions. An analysis of the different classes of focus-refined complex I showed that structural switches due to quinone reduction led to the formation of a novel channel that could transfer reduced quinones to the intercomplex substrate pool. Innovation and Conclusion: Our results indicate potential mechanism for the facilitated electron transfer involving a dynamic substrate pool and intercomplex movement by which supercomplexes play an active role in the regulation of metabolic flux and reactive oxygen species.

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Primary Citation of related structures