7DGQ image
Deposition Date 2020-11-12
Release Date 2022-05-18
Last Version Date 2026-08-12
Entry Detail
PDB ID:
7DGQ
Keywords:
Title:
Activity optimized supercomplex state1
Biological Source:
Source Organism(s):
Bos taurus (Taxon ID: 9913)
Method Details:
Experimental Method:
Resolution:
5.00 Å
Aggregation State:
TISSUE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductas
Gene (Uniprot):MT-ND1
Chain IDs:B (auth: 1)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductas
Gene (Uniprot):MT-ND2
Chain IDs:H (auth: 2)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductas
Gene (Uniprot):MT-ND3
Chain IDs:A (auth: 3)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductas
Gene (Uniprot):MT-ND4
Chain IDs:E (auth: 4)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductas
Gene (Uniprot):MT-ND4L
Chain IDs:F (auth: 5)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductas
Gene (Uniprot):MT-ND5
Chain IDs:G (auth: 6)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductas
Gene (Uniprot):MT-ND6
Chain IDs:D (auth: 7)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFV1
Chain IDs:I (auth: 8)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFV2
Chain IDs:C (auth: 9)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductas
Gene (Uniprot):NDUFS1
Chain IDs:W (auth: A)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX7C
Chain IDs:U (auth: A0)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX5B
Chain IDs:O (auth: A5)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX6A2
Chain IDs:P (auth: A6)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX4I1
Chain IDs:M (auth: A7)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX8B
Chain IDs:V (auth: A8)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):MT-CO3
Chain IDs:L (auth: A9)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFS2
Chain IDs:X (auth: B)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX7A1
Chain IDs:S (auth: B2)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX7B
Chain IDs:T (auth: B3)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX5A
Chain IDs:N (auth: B4)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFS3
Chain IDs:Y (auth: C)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX6B1
Chain IDs:Q (auth: C0)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):MT-CO2
Chain IDs:K (auth: C1)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):COX6C
Chain IDs:R (auth: C2)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit
Gene (Uniprot):MT-CO1
Chain IDs:J (auth: C3)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFS7
Chain IDs:Z (auth: D)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFS8
Chain IDs:AA (auth: E)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFV3
Chain IDs:BA (auth: F)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFS4
Chain IDs:CA (auth: G)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFS5
Chain IDs:DA (auth: H)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFS6
Chain IDs:EA (auth: I)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA1
Chain IDs:FA (auth: J)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA2
Chain IDs:GA (auth: K)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA3
Chain IDs:HA (auth: L)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA5
Chain IDs:IA (auth: N)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA6
Chain IDs:JA (auth: O)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA7
Chain IDs:KA (auth: P)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA8
Chain IDs:LA (auth: Q)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA9
Chain IDs:MA (auth: R)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA10
Chain IDs:NA (auth: S)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA11
Chain IDs:OA (auth: T)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA12
Chain IDs:PA (auth: U)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFA13
Chain IDs:QA (auth: V)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein, mitocho
Gene (Uniprot):NDUFAB1
Chain IDs:RA (auth: W), FB (auth: M)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB1
Chain IDs:SA (auth: X)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB2
Chain IDs:TA (auth: Y)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB3
Chain IDs:UA (auth: Z)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB4
Chain IDs:VA (auth: a)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB5
Chain IDs:WA (auth: b)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB6
Chain IDs:XA (auth: c)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB7
Chain IDs:YA (auth: d)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB8
Chain IDs:EB (auth: e)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB9
Chain IDs:ZA (auth: f)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB10
Chain IDs:DB (auth: g)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFB11
Chain IDs:AB (auth: h)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFC1
Chain IDs:BB (auth: i)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinon
Gene (Uniprot):NDUFC2
Chain IDs:CB (auth: j)
Chain Length:0
Number of Molecules:1
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCRC1
Chain IDs:GB (auth: k), RB (auth: w)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCRC2
Chain IDs:HB (auth: l), SB (auth: x)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b
Gene (Uniprot):MT-CYB
Chain IDs:IB (auth: m), TB (auth: y)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c1, heme protein,
Gene (Uniprot):CYC1
Chain IDs:JB (auth: o), UB (auth: z)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCRFS1
Chain IDs:KB (auth: p), VB (auth: A1)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCRB
Chain IDs:LB (auth: q), WB (auth: A2)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCRQ
Chain IDs:MB (auth: r), XB (auth: A3)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCRH
Chain IDs:NB (auth: s), YB (auth: B7)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCR11
Chain IDs:OB (auth: t), ZB (auth: A4)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCR10
Chain IDs:PB (auth: u), AC (auth: B6)
Chain Length:0
Number of Molecules:2
Biological Source:Bos taurus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b-c1 complex subun
Gene (Uniprot):UQCRFS1
Chain IDs:QB (auth: v), BC (auth: B5)
Chain Length:0
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
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