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: https://doi.org/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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C73Sus scrofaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial464Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1SZP7 (Sus scrofa)
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UniProt GroupA0A4X1SZP7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial463Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1S1A8 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial264Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial249Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SM98 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial123Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1S031 (Sus scrofa)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial727Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1V1H9 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial212Sus scrofaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial216Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1TL60 (Sus scrofa)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial175Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
K, R
145Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial377Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7113Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5116Sus scrofaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrial
O, X
156Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 299Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6128Sus scrofaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 170Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 384Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1VPG4 (Sus scrofa)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial357Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SIS9 (Sus scrofa)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11141Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13144Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial105Sus scrofaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 398Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A4X1VBN1 (Sus scrofa)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialAA [auth a]189Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6BA [auth b]128Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialCA [auth c]186Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10DA [auth d]176Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialEA [auth e]154Sus scrofaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialFA [auth f]76Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2GA [auth g]122Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5HA [auth h]106Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2IA [auth i]347Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O79875 (Sus scrofa)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3JA [auth j]115Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O79880 (Sus scrofa)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LKA [auth k]98Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5LA [auth l]606Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6MA [auth m]175Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1NA [auth n]58Sus scrofaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4OA [auth o]129Sus scrofaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9PA [auth p]179Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4QA [auth q]459Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1RA [auth r]318Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8SA [auth s]172Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7TA [auth t]137Sus scrofaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialFB [auth 5],
UA [auth u]
480Sus scrofaMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialGB [auth 6],
VA [auth v]
453Sus scrofaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bHB [auth 7],
WA [auth w]
379Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialIB [auth 8],
XA [auth x]
326Sus scrofaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7JB [auth 9],
YA [auth y]
111Sus scrofaMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8KB [auth Aa],
ZA [auth z]
82Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4X1UYT9 (Sus scrofa)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialAB [auth 0],
LB [auth Ab]
91Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1S3W0 (Sus scrofa)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9BB [auth 1],
MB [auth Ac]
64Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q2EN79 (Sus scrofa)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialCB [auth 2],
EB [auth 4]
274Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1RNZ1 (Sus scrofa)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10DB [auth 3],
NB [auth Ad]
56Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1SDI2 (Sus scrofa)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrialOB [auth Ae],
PB [auth Af]
78Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1RNZ1 (Sus scrofa)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialQB [auth Ag]46Sus scrofaMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialRB [auth Ah]59Sus scrofaMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialSB [auth Ai]56Sus scrofaMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialTB [auth Aj]47Sus scrofaMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1UB [auth Ak]514Sus scrofaMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2VB [auth Al]227Sus scrofaMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3WB [auth Am]261Sus scrofaMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialXB [auth An]147Sus scrofaMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialYB [auth Ao]109Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F1SJ34 (Sus scrofa)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialZB [auth Ap]98Sus scrofaMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A, mitochondrialAC [auth Aq]84Sus scrofaMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1BC [auth Ar]85Sus scrofaMutation(s): 0 
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Small Molecules
Ligands 14 Unique
IDChains Name / 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
HEA
Query on HEA

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

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

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DC [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
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-UHFFFAOYSA-N
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
ZN
Query on ZN

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

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.9

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