7DGQ

Activity optimized supercomplex state1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A Dynamic Substrate Pool Revealed by cryo-EM of a Lipid-Preserved Respiratory Supercomplex.

Jeon, T.J.Lee, S.G.Yoo, S.H.Kim, M.Song, D.Ryu, J.Park, H.Kim, D.S.Hyun, J.Kim, H.M.Ryu, S.E.

(2022) Antioxid Redox Signal 

  • DOI: https://doi.org/10.1089/ars.2021.0114
  • Primary Citation of Related Structures:  
    7DGQ, 7DGR, 7DGS, 7DGZ, 7DH0, 7DKF

  • PubMed Abstract: 

    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 I 1 III 2 IV 1 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.


  • Organizational Affiliation

    Department of Bioscience and Biotechnology, Sejong University, Seoul, Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A [auth 3]115Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1B [auth 1]318Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialC [auth 9]217Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6D [auth 7]175Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4E [auth 4]459Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LF [auth 5]98Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5G [auth 6]606Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2H [auth 2]347Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialI [auth 8]444Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1J [auth C3]514Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2K [auth C1]227Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3L [auth A9]261Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialM [auth A7]169Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialN [auth B4]152Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialO [auth A5]129Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialP [auth A6]97Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1Q [auth C0]86Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CR [auth C2]74Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialS [auth B2]80Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialT [auth B3]80Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialU [auth A0]63Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialV [auth A8]70Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialW [auth A]704Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialX [auth B]430Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialY [auth C]228Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialZ [auth D]179Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialAA [auth E]176Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialBA [auth F]75Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialCA [auth G]133Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5DA [auth H]105Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialEA [auth I]96Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1FA [auth J]70Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2GA [auth K]98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3HA [auth L]83Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5IA [auth N]115Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6JA [auth O]127Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7KA [auth P]112Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8LA [auth Q]171Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialMA [auth R]345Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialNA [auth S]320Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11OA [auth T]140Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12PA [auth U]145Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13QA [auth V]143Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialFB [auth M],
RA [auth W]
86Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1SA [auth X]57Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialTA [auth Y]72Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3UA [auth Z]98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4VA [auth a]128Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialWA [auth b]143Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6XA [auth c]128Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7YA [auth d]117Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9ZA [auth f]178Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialAB [auth h]125Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialBB [auth i]49Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2CB [auth j]120Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10DB [auth g]176Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialEB [auth e]158Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialGB [auth k],
RB [auth w]
480Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialHB [auth l],
SB [auth x]
453Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bIB [auth m],
TB [auth y]
379Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialJB [auth o],
UB [auth z]
325Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialKB [auth p],
VB [auth A1]
196Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7LB [auth q],
WB [auth A2]
111Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8MB [auth r],
XB [auth A3]
82Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialNB [auth s],
YB [auth B7]
91Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10OB [auth t],
ZB [auth A4]
56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9AC [auth B6],
PB [auth u]
64Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialBC [auth B5],
QB [auth v]
78Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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AD [auth J],
ED [auth b],
GC [auth 6]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA (Subject of Investigation/LOI)
Query on HEA

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MC [auth C3],
NC [auth C3]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1 (Subject of Investigation/LOI)
Query on PC1

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BD [auth Q],
CC [auth 3],
DD [auth S],
FD [auth j],
IC [auth 2]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE (Subject of Investigation/LOI)
Query on 3PE

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DC [auth 1],
FC [auth 4],
GD [auth j],
HC [auth 2],
VC [auth B]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NAP
Query on NAP

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CD [auth R]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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KD [auth o],
ND [auth z]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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HD [auth m],
ID [auth m],
LD [auth y],
MD [auth y]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FMN (Subject of Investigation/LOI)
Query on FMN

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JC [auth 8]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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KC [auth 8]
SC [auth A]
TC [auth A]
WC [auth D]
XC [auth E]
KC [auth 8],
SC [auth A],
TC [auth A],
WC [auth D],
XC [auth E],
YC [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UQ2
Query on UQ2

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OD [auth A2]UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
FES
Query on FES

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EC [auth 9],
JD [auth m],
UC [auth A]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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RC [auth A5],
ZC [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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LC [auth C3],
PC [auth C1],
QC [auth C1]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

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OC [auth C1]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release