5GUP

Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Sus scrofa
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMmpstruc

  • Deposited: 2016-08-30 Released: 2017-03-29 
  • Deposition Author(s): Gu, J., Wu, M., Guo, R., Yang, M.
  • Funding Organization(s): Ministry of Science and Technology of China, National Outstanding Young Scholar Science Foundation, National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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

Structure of Mammalian Respiratory Supercomplex I1III2IV1

Wu, M.Gu, J.Guo, R.Huang, Y.Yang, M.

(2016) Cell 167: 1598-1609.e10

  • DOI: 10.1016/j.cell.2016.11.012
  • Primary Citation of Related Structures:  
    5GUP

  • PubMed Abstract: 
  • The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown ...

    The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCI 1 III 2 IV 1 . The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration.


    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. Electronic address: maojunyang@tsinghua.edu.cn.



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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CA73Sus scrofaMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialB464Sus scrofaMutation(s): 0 
Gene Names: NDUFV1
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 3
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialC463Sus scrofaMutation(s): 0 
Gene Names: NDUFS2
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialD264Sus scrofaMutation(s): 0 
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Entity ID: 5
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NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialE249Sus scrofaMutation(s): 0 
Gene Names: NDUFV2
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Entity ID: 6
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialF123Sus scrofaMutation(s): 0 
Gene Names: NDUFS6
Membrane Entity: Yes 
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Entity ID: 7
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NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialG727Sus scrofaMutation(s): 0 
Gene Names: NDUFS1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialH212Sus scrofaMutation(s): 0 
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Entity ID: 9
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialI216Sus scrofaMutation(s): 0 
Gene Names: NDUFS7
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialJ175Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12K, R145Sus scrofaMutation(s): 0 
Gene Names: NDUFA12
Membrane Entity: Yes 
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Entity ID: 12
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialL377Sus scrofaMutation(s): 0 
Gene Names: NDUFA9
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Entity ID: 13
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7M113Sus scrofaMutation(s): 0 
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5N116Sus scrofaMutation(s): 0 
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Entity ID: 15
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Acyl carrier protein, mitochondrialO, X156Sus scrofaMutation(s): 0 
Gene Names: NDUFAB1
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Entity ID: 16
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2P99Sus scrofaMutation(s): 0 
Gene Names: NDUFA2
Membrane Entity: Yes 
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6Q128Sus scrofaMutation(s): 0 
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1S70Sus scrofaMutation(s): 0 
Gene Names: NDUFA1
Membrane Entity: Yes 
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Entity ID: 19
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3T84Sus scrofaMutation(s): 0 
Gene Names: NDUFA3
Membrane Entity: Yes 
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Entity ID: 20
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialU357Sus scrofaMutation(s): 0 
Gene Names: NDUFA10
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Entity ID: 21
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11V141Sus scrofaMutation(s): 0 
Gene Names: NDUFA11
Membrane Entity: Yes 
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Entity ID: 22
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13W144Sus scrofaMutation(s): 0 
Gene Names: NDUFA13
Membrane Entity: Yes 
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Entity ID: 23
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialY105Sus scrofaMutation(s): 0 
Gene Names: NDUFB2
Membrane Entity: Yes 
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Entity ID: 24
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3Z98Sus scrofaMutation(s): 0 
Gene Names: NDUFB3
Membrane Entity: Yes 
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Entity ID: 25
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialAA [auth a]189Sus scrofaMutation(s): 0 
Gene Names: NDUFB5
Membrane Entity: Yes 
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Entity ID: 26
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6BA [auth b]128Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialCA [auth c]186Sus scrofaMutation(s): 0 
Gene Names: NDUFB8
Membrane Entity: Yes 
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Entity ID: 28
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10DA [auth d]176Sus scrofaMutation(s): 0 
Gene Names: NDUFB10
Membrane Entity: Yes 
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialEA [auth e]154Sus scrofaMutation(s): 0 
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NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialFA [auth f]76Sus scrofaMutation(s): 0 
Gene Names: MGARP
Membrane Entity: Yes 
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Entity ID: 31
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NADH dehydrogenase [ubiquinone] 1 subunit C2GA [auth g]122Sus scrofaMutation(s): 0 
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Entity ID: 32
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NADH dehydrogenase [ubiquinone] iron-sulfur protein 5HA [auth h]106Sus scrofaMutation(s): 0 
Gene Names: NDUFS5
Membrane Entity: Yes 
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Entity ID: 33
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NADH-ubiquinone oxidoreductase chain 2IA [auth i]347Sus scrofaMutation(s): 0 
Gene Names: MT-ND2MTND2NADH2ND2
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 34
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NADH-ubiquinone oxidoreductase chain 3JA [auth j]115Sus scrofaMutation(s): 0 
Gene Names: MT-ND3MTND3NADH3ND3
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 35
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NADH-ubiquinone oxidoreductase chain 4LKA [auth k]98Sus scrofaMutation(s): 0 
Gene Names: MT-ND4LMTND4LNADH4LND4L
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 36
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NADH-ubiquinone oxidoreductase chain 5LA [auth l]606Sus scrofaMutation(s): 0 
Gene Names: MT-ND5MTND5NADH5ND5
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 37
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NADH-ubiquinone oxidoreductase chain 6MA [auth m]175Sus scrofaMutation(s): 0 
Gene Names: MT-ND6MTND6NADH6ND6
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 38
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1NA [auth n]58Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 39
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4OA [auth o]129Sus scrofaMutation(s): 0 
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Entity ID: 40
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9PA [auth p]179Sus scrofaMutation(s): 0 
Gene Names: NDUFB9
Membrane Entity: Yes 
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Entity ID: 41
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NADH-ubiquinone oxidoreductase chain 4QA [auth q]459Sus scrofaMutation(s): 0 
Gene Names: MT-ND4MTND4NADH4ND4
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 42
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NADH-ubiquinone oxidoreductase chain 1RA [auth r]318Sus scrofaMutation(s): 0 
Gene Names: MT-ND1MTND1NADH1ND1
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 43
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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8SA [auth s]172Sus scrofaMutation(s): 0 
Gene Names: NDUFA8
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Entity ID: 44
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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7TA [auth t]137Sus scrofaMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialFB [auth 5],
UA [auth u]
480Sus scrofaMutation(s): 0 
Gene Names: UQCRC1
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialGB [auth 6],
VA [auth v]
453Sus scrofaMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bHB [auth 7],
WA [auth w]
379Sus scrofaMutation(s): 0 
Gene Names: cytbCYTBCytB
Membrane Entity: Yes 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialIB [auth 8],
XA [auth x]
326Sus scrofaMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7JB [auth 9],
YA [auth y]
111Sus scrofaMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8KB [auth Aa],
ZA [auth z]
82Sus scrofaMutation(s): 0 
Gene Names: UQCRQ
Membrane Entity: Yes 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialAB [auth 0],
LB [auth Ab]
91Sus scrofaMutation(s): 0 
Gene Names: LOC100524873
Membrane Entity: Yes 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9BB [auth 1],
MB [auth Ac]
64Sus scrofaMutation(s): 0 
Gene Names: UQCR10
Membrane Entity: Yes 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialCB [auth 2],
EB [auth 4]
274Sus scrofaMutation(s): 0 
Gene Names: UQCRFS1
Membrane Entity: Yes 
UniProt
Find proteins for F1RNZ1 (Sus scrofa)
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10DB [auth 3],
NB [auth Ad]
56Sus scrofaMutation(s): 0 
Gene Names: LOC100524239
Membrane Entity: Yes 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrialOB [auth Ae],
PB [auth Af]
78Sus scrofaMutation(s): 0 
Gene Names: UQCRFS1
Membrane Entity: Yes 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialQB [auth Ag]46Sus scrofaMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialRB [auth Ah]59Sus scrofaMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialSB [auth Ai]56Sus scrofaMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialTB [auth Aj]47Sus scrofaMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1UB [auth Ak]514Sus scrofaMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2VB [auth Al]227Sus scrofaMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3WB [auth Am]261Sus scrofaMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialXB [auth An]147Sus scrofaMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialYB [auth Ao]109Sus scrofaMutation(s): 0 
Gene Names: COX5A
Membrane Entity: Yes 
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Entity ID: 65
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Cytochrome c oxidase subunit 5B, mitochondrialZB [auth Ap]98Sus scrofaMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A, mitochondrialAC [auth Aq]84Sus scrofaMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1BC [auth Ar]85Sus scrofaMutation(s): 0 
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Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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FD [auth x],
GD [auth z],
MD [auth 5],
OC [auth V],
SD [auth 8],
FD [auth x],
GD [auth z],
MD [auth 5],
OC [auth V],
SD [auth 8],
UC [auth i],
UD [auth Aa],
WC [auth l],
YC [auth s],
ZC [auth u]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
HEA
Query on HEA

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VD [auth Ak],
WD [auth Ak]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PLX
Query on PLX

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HD [auth 2],
KC [auth H],
KD [auth 4],
PC [auth V],
TC [auth i]
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
 Ligand Interaction
NDP
Query on NDP

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MC [auth L]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
PEE
Query on PEE

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AD [auth u],
DD [auth w],
ID [auth 2],
ND [auth 5],
OD [auth 7],
AD [auth u],
DD [auth w],
ID [auth 2],
ND [auth 5],
OD [auth 7],
PD [auth 7],
QC [auth W],
SC [auth i],
VC [auth l],
XC [auth q]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
HEC
Query on HEC

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ED [auth x],
TD [auth 8]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

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BD [auth w],
CD [auth w],
QD [auth 7],
RD [auth 7]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
ZMP
Query on ZMP

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NC [auth Q],
RC [auth X]
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
 Ligand Interaction
FMN
Query on FMN

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

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CC [auth B],
FC [auth G],
GC [auth G],
IC [auth H],
JC [auth H],
CC [auth B],
FC [auth G],
GC [auth G],
IC [auth H],
JC [auth H],
LC [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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EC [auth E],
HC [auth G],
JD [auth 2],
LD [auth 4]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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BE [auth Ap]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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AE [auth Al],
XD [auth Ak],
ZD [auth Al]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2016YFA0501100 and 2012CB911101
National Outstanding Young Scholar Science FoundationChina--
National Natural Science Foundation of ChinaChina3162500065, 31030020 and 31170679

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other