5GPN

Architecture of mammalian respirasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The architecture of the mammalian respirasome.

Gu, J.Wu, M.Guo, R.Yan, K.Lei, J.Gao, N.Yang, M.

(2016) Nature 537: 639-643

  • DOI: 10.1038/nature19359
  • Primary Citation of Related Structures:  
    5GPN

  • PubMed Abstract: 
  • The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown ...

    The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown. Here we report a 5.4 Å cryo-electron microscopy structure of the major 1.7 megadalton SCI1III2IV1 respirasome purified from porcine heart. The CIII dimer and CIV bind at the same side of the L-shaped CI, with their transmembrane domains essentially aligned to form a transmembrane disk. Compared to free CI, the CI in the respirasome is more compact because of interactions with CIII and CIV. The NDUFA11 and NDUFB9 supernumerary subunits of CI contribute to the oligomerization of CI and CIII. The structure of the respirasome provides information on the precise arrangements of the respiratory chain complexes in mitochondria.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA, M446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB, N439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC, O379Bos taurusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD, P241Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE, Q274Bos taurusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F, R110Bos taurusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G, S81Bos taurusMutation(s): 0 
Gene Names: UQCRQ
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH, T78Bos taurusMutation(s): 0 
Gene Names: UQCRH
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI, U78Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9J, L62Bos taurusMutation(s): 0 
Gene Names: UQCR10
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10K, V56Bos taurusMutation(s): 0 
Gene Names: UQCR11UQCR
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3W264Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunitX [auth Y]727Sus scrofaMutation(s): 0 
Gene Names: NDUFS1
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Entity ID: 14
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 2Y [auth Z]463Sus scrofaMutation(s): 0 
Gene Names: NDUFS2
Membrane Entity: Yes 
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Entity ID: 15
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 7Z [auth a]216Sus scrofaMutation(s): 0 
Gene Names: NDUFS7
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8AA [auth b]212Sus scrofaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialBA [auth c]464Sus scrofaMutation(s): 0 
Gene Names: NDUFV1
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 18
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NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialCA [auth d]249Sus scrofaMutation(s): 0 
Gene Names: NDUFV2
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1DA [auth e]318Sus scrofaMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2EA [auth f]347Sus scrofaMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3FA [auth g]115Sus scrofaMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4GA [auth h]459Sus scrofaMutation(s): 0 
Gene Names: MT-ND4MTND4NADH4ND4
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LHA [auth i]98Sus scrofaMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5IA [auth j]606Sus scrofaMutation(s): 0 
Gene Names: MT-ND5MTND5NADH5ND5
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6JA [auth k],
KA [auth l]
175Sus scrofaMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3LA [auth m]84Sus scrofaMutation(s): 0 
Gene Names: NDUFA3
Membrane Entity: Yes 
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Entity ID: 27
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2MA [auth n]99Sus scrofaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5NA [auth o]106Sus scrofaMutation(s): 0 
Gene Names: NDUFS5
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9OA [auth p]377Sus scrofaMutation(s): 0 
Gene Names: NDUFA9
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialPA [auth q],
TA [auth v]
357Sus scrofaMutation(s): 0 
Gene Names: NDUFA10
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13QA [auth r]144Sus scrofaMutation(s): 0 
Gene Names: NDUFA13
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier proteinJB [auth Aa],
RA [auth t]
156Sus scrofaMutation(s): 0 
Gene Names: NDUFAB1
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5RB [auth Ai],
SA [auth u]
189Sus scrofaMutation(s): 0 
Gene Names: NDUFB5
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial NADH dehydrogenase Fe-S protein 4UA [auth w]175Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialVA [auth x]123Sus scrofaMutation(s): 0 
Gene Names: NDUFS6
Membrane Entity: Yes 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3WA [auth 0]261Bos taurusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialXA [auth 1]147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialYA [auth 2]109Bos taurusMutation(s): 0 
Gene Names: COX5A
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialZA [auth 3]98Bos taurusMutation(s): 0 
Gene Names: COX5B
Membrane Entity: Yes 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialAB [auth 4]84Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1BB [auth 5]85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CCB [auth 6]73Bos taurusMutation(s): 0 
Gene Names: COX6C
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialDB [auth 7]59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
Membrane Entity: Yes 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialEB [auth 8]56Bos taurusMutation(s): 0 
Gene Names: COX7B
Membrane Entity: Yes 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialFB [auth 9]47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
Membrane Entity: Yes 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialGB [auth s]46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
Membrane Entity: Yes 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1HB [auth y]514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2IB [auth z]227Bos taurusMutation(s): 0 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragmentKB [auth Ab],
QB [auth Ah]
134Sus scrofaMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1LB [auth Ac]70Sus scrofaMutation(s): 0 
Gene Names: NDUFA1
Membrane Entity: Yes 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragmentMB [auth Ad],
XB [auth Ao],
YB [auth Ap],
EC [auth Av]
43Sus scrofaMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5NB [auth Ae]116Sus scrofaMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6OB [auth Af]128Sus scrofaMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11PB [auth Ag]141Sus scrofaMutation(s): 0 
Gene Names: NDUFA11
Membrane Entity: Yes 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10SB [auth Aj]176Sus scrofaMutation(s): 0 
Gene Names: NDUFB10
Membrane Entity: Yes 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9TB [auth Ak]178Sus scrofaMutation(s): 0 
Gene Names: NDUFB9
Membrane Entity: Yes 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2UB [auth Al]122Sus scrofaMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1VB [auth Am]76Sus scrofaMutation(s): 0 
Gene Names: MGARP
Membrane Entity: Yes 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8WB [auth An]172Sus scrofaMutation(s): 0 
Gene Names: NDUFA8
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragmentZB [auth Aq],
BC [auth As],
FC [auth Aw]
76Sus scrofaMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragmentAC [auth Ar]34Sus scrofaMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragmentCC [auth At]17Sus scrofaMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragmentDC [auth Au]13Sus scrofaMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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AD [auth y],
ZC [auth y]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
NDP
Query on NDP

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XC [auth p]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
HEC
Query on HEC

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IC [auth D],
MC [auth P]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

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GC [auth C],
HC [auth C],
KC [auth O],
LC [auth O]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FMN
Query on FMN

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VC [auth c]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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OC [auth Y],
PC [auth Y],
RC [auth a],
SC [auth b],
TC [auth b],
OC [auth Y],
PC [auth Y],
RC [auth a],
SC [auth b],
TC [auth b],
UC [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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JC [auth E],
NC [auth Q],
QC [auth Y],
WC [auth d]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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YC [auth 3]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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BD [auth y],
DD [auth z],
ED [auth z]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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CD [auth y]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31030020 and 31170679
Ministry of Science and TechnologyChina2012CB911101

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Refinement description