7DGR

Activity optimized supercomplex state2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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 Bioengineering, College of Engineering, Hanyang University, Seoul, Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialA [auth 9]217Bos 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 4B [auth 4]459Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2C [auth 2]347Bos 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 5E [auth 6]606Bos 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 3G [auth 3]115Bos 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 1H [auth 1]318Bos 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
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialJ [auth A]704Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialK [auth B]430Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialL [auth C]228Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialM [auth D]179Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialN [auth E]176Bos taurusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialO [auth F]75Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialP [auth G]133Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5Q [auth H]105Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR [auth I]96Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1S [auth J]70Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2T [auth K]98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3U [auth L]83Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5V [auth N]115Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6W [auth O]127Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7X [auth P]112Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8Y [auth Q]171Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialZ [auth R]345Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialAA [auth S]320Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11BA [auth T]140Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12CA [auth U]145Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13DA [auth V]143Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialEA [auth W],
SA [auth M]
88Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1FA [auth X]57Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialGA [auth Y]72Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3HA [auth Z]98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4IA [auth a]128Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialJA [auth b]143Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6KA [auth c]128Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7LA [auth d]117Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9MA [auth f]178Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialNA [auth h]125Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialOA [auth i]49Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2PA [auth j]120Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10QA [auth g]176Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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UniProt GroupQ02373
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialRA [auth e]158Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialEB [auth w],
TA [auth k]
480Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialFB [auth x],
UA [auth l]
453Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bGB [auth y],
VA [auth m]
379Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialHB [auth z],
WA [auth o]
241Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialIB [auth A0],
XA [auth p]
196Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7JB [auth A1],
YA [auth q]
111Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8KB [auth A2],
ZA [auth r]
82Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialAB [auth s],
LB [auth B3]
91Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10BB [auth t],
MB [auth A3]
56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9CB [auth u],
NB [auth B2]
64Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialDB [auth v],
OB [auth B1]
78Bos taurusMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1PB [auth A9]514Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2QB [auth C4]227Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3RB [auth C2]261Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialSB [auth A7]169Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialTB [auth C0]152Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialUB [auth A6]129Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialVB [auth A4]97Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1WB [auth A5]86Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CXB [auth B4]74Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialYB [auth C3]80Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialZB [auth B0]80Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialAC [auth C1]63Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialBC [auth A8]70Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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EC [auth 4],
JC [auth 6],
UC [auth J]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA (Subject of Investigation/LOI)
Query on HEA

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GD [auth A9],
HD [auth A9]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1 (Subject of Investigation/LOI)
Query on PC1

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GC [auth 4],
IC [auth 2],
VC [auth L],
XC [auth S],
YC [auth j]
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 4],
FC [auth 4],
HC [auth 2],
PC [auth B]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NAP
Query on NAP

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WC [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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CD [auth o],
FD [auth z]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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AD [auth m],
DD [auth y],
ED [auth y],
ZC [auth m]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FMN (Subject of Investigation/LOI)
Query on FMN

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

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LC [auth 8]
MC [auth A]
NC [auth A]
QC [auth D]
RC [auth E]
LC [auth 8],
MC [auth A],
NC [auth A],
QC [auth D],
RC [auth E],
SC [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N