8PW6

C respirasome from murine liver


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

SCAF1 drives the compositional diversity of mammalian respirasomes.

Vercellino, I.Sazanov, L.A.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01255-0
  • Primary Citation of Related Structures:  
    8PW5, 8PW6, 8PW7, 8RGP, 8RGQ, 8RGR, 8RGT

  • PubMed Abstract: 

    Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII 2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIII 2 CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.


  • Organizational Affiliation

    Institute of Science and Technology Austria, Klosterneuburg, Austria.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA,
K [auth L]
480Mus musculusMutation(s): 0 
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IMPC:  MGI:107876
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB,
L [auth M]
453Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC,
M [auth N]
381Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD,
N [auth O]
325Mus musculusMutation(s): 0 
EC: 7.1.1.8
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IMPC:  MGI:1913695
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
O [auth P],
U [auth T]
274Mus musculusMutation(s): 0 
EC: 7.1.1.8
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F,
P [auth Q]
111Mus musculusMutation(s): 0 
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IMPC:  MGI:1914780
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G,
Q [auth R]
82Mus musculusMutation(s): 0 
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IMPC:  MGI:107807
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH,
R [auth S]
89Mus musculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9I [auth J],
S [auth U]
64Mus musculusMutation(s): 0 
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IMPC:  MGI:1913402
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10J [auth K],
T [auth V]
56Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1V [auth n]514Mus musculusMutation(s): 0 
EC: 7.1.1.9
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2W [auth o]227Mus musculusMutation(s): 0 
EC: 7.1.1.9
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3X [auth p]261Mus musculusMutation(s): 0 
EC: 7.1.1.9
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialY [auth q]169Mus musculusMutation(s): 0 
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IMPC:  MGI:88473
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialZ [auth r]146Mus musculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialAA [auth s]128Mus musculusMutation(s): 0 
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IMPC:  MGI:88475
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialBA [auth t]97Mus musculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1CA [auth u]86Mus musculusMutation(s): 0 
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IMPC:  MGI:107460
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CDA [auth v]76Mus musculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialEA [auth x]80Mus musculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialFA [auth y]63Mus musculusMutation(s): 0 
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IMPC:  MGI:103226
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialGA [auth z]70Mus musculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A2, mitochondrialHA [auth w]83Mus musculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialIA [auth 6]224Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:1922656
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialJA [auth C1]263Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:1915599
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialKA [auth D1]463Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:2385112
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialLA [auth 2]248Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:1920150
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialMA [auth 1]464Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:107851
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialNA [auth 3]727Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:2443241
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialOA [auth 9]212Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:2385079
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialPA [auth P1]377Mus musculusMutation(s): 0 
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IMPC:  MGI:1913358
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialQA [auth Q1]175Mus musculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialRA [auth 7]116Mus musculusMutation(s): 0 
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IMPC:  MGI:107932
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2SA [auth S1]99Mus musculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialHB [auth U1],
TA [auth T1]
156Mus musculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5UA [auth V1]116Mus musculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6VA [auth W1]131Mus musculusMutation(s): 0 
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IMPC:  MGI:1914380
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12WA [auth q1]145Mus musculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7XA [auth r1]113Mus musculusMutation(s): 0 
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IMPC:  MGI:1913666
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialYA [auth s1]104Mus musculusMutation(s): 0 
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IMPC:  MGI:1890894
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3ZA [auth A1]115Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1AB [auth H1]318Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6BB [auth J1]172Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LCB [auth K1]98Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5DB [auth L1]607Mus musculusMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4EB [auth M1]459Mus musculusMutation(s): 0 
EC: 7.1.1.2
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2FB [auth N1]345Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialGB [auth O1]355Mus musculusMutation(s): 0 
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IMPC:  MGI:1914523
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8IB [auth X1]172Mus musculusMutation(s): 0 
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IMPC:  MGI:1915625
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11JB [auth Y1]141Mus musculusMutation(s): 0 
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IMPC:  MGI:1917125
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13KB [auth Z1]144Mus musculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1LB [auth a1]70Mus musculusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3MB [auth b1]84Mus musculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialNB [auth c1]76Mus musculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2OB [auth d1]120Mus musculusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5PB [auth e1]106Mus musculusMutation(s): 0 
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IMPC:  MGI:1890889
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1QB [auth f1]57Mus musculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialRB [auth g1]151Mus musculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialSB [auth h1]189Mus musculusMutation(s): 0 
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IMPC:  MGI:1913296
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6TB [auth i1]128Mus musculusMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialUB [auth j1]105Mus musculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3VB [auth k1]104Mus musculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialWB [auth l1]186Mus musculusMutation(s): 0 
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IMPC:  MGI:1914514
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4XB [auth m1]129Mus musculusMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9YB [auth n1]179Mus musculusMutation(s): 0 
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IMPC:  MGI:1913468
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7ZB [auth o1]137Mus musculusMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10AC [auth p1]176Mus musculusMutation(s): 0 
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Small Molecules
Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AD [auth R]
BF [auth N1]
CC [auth A]
DD [auth V]
FF [auth Y1]
AD [auth R],
BF [auth N1],
CC [auth A],
DD [auth V],
FF [auth Y1],
GC [auth C],
IF [auth Y1],
KC [auth D],
KF [auth a1],
LF [auth d1],
OF [auth h1],
PC [auth L],
SE [auth H1],
VE [auth L1],
WE [auth L1],
YC [auth R],
ZC [auth R]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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VD [auth y]TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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GD [auth n],
HD [auth n]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC1
Query on PC1

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CD [auth V]
KE [auth 9]
LE [auth 9]
MC [auth E]
NC [auth K]
CD [auth V],
KE [auth 9],
LE [auth 9],
MC [auth E],
NC [auth K],
OD [auth p],
PD [auth p],
PE [auth A1],
QC [auth L],
WD [auth z],
YE [auth M1],
ZD [auth 6]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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AE [auth D1]
AF [auth M1]
BC [auth A]
BD [auth R]
CF [auth N1]
AE [auth D1],
AF [auth M1],
BC [auth A],
BD [auth R],
CF [auth N1],
FC [auth C],
GF [auth Y1],
HC [auth C],
HF [auth Y1],
IC [auth C],
ID [auth n],
JD [auth n],
JF [auth Z1],
LD [auth o],
MF [auth d1],
ND [auth p],
NF [auth d1],
OC [auth L],
PF [auth i1],
QD [auth q],
QE [auth A1],
RC [auth N],
RE [auth H1],
SD [auth t],
TD [auth v],
TE [auth K1],
UC [auth N],
UD [auth x],
UE [auth L1],
WC [auth P],
XE [auth L1],
YD [auth 6],
ZE [auth M1]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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ME [auth P1]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEC
Query on HEC

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JC [auth D],
VC [auth O]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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DC [auth C],
EC [auth C],
SC [auth N],
TC [auth N]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZMP
Query on ZMP

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OE [auth W1],
QF [auth n1]
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
DGT
Query on DGT

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DF [auth O1]2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
FMN
Query on FMN

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CE [auth 1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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DE [auth 1]
EE [auth 3]
FE [auth 3]
IE [auth 9]
JE [auth 9]
DE [auth 1],
EE [auth 3],
FE [auth 3],
IE [auth 9],
JE [auth 9],
XD [auth 6]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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BE [auth 2],
GE [auth 3],
LC [auth E],
XC [auth P]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA
Query on CUA

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MD [auth o]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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NE [auth 7],
RD [auth s]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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ED [auth n]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
K
Query on K

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HE [auth 3]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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EF [auth O1],
KD [auth o]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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FD [auth n]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
KA [auth D1]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
AYA
Query on AYA
XA [auth r1]L-PEPTIDE LINKINGC5 H9 N O3ALA
FME
Query on FME
ZA [auth A1]L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
TB [auth i1]L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19_4092:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101020697

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release