5Z62

Structure of human cytochrome c oxidase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Structure of the intact 14-subunit human cytochrome c oxidase.

Zong, S.Wu, M.Gu, J.Liu, T.Guo, R.Yang, M.

(2018) Cell Res 28: 1026-1034

  • DOI: https://doi.org/10.1038/s41422-018-0071-1
  • Primary Citation of Related Structures:  
    5Z62

  • PubMed Abstract: 

    Respiration is one of the most basic features of living organisms, and the electron transport chain complexes are probably the most complicated protein system in mitochondria. Complex-IV is the terminal enzyme of the electron transport chain, existing either as randomly scattered complexes or as a component of supercomplexes. NDUFA4 was previously assumed as a subunit of complex-I, but recent biochemical data suggested it may be a subunit of complex-IV. However, no structural evidence supporting this notion was available till now. Here we obtained the 3.3 Å resolution structure of complex-IV derived from the human supercomplex I 1 III 2 IV 1 and assigned the NDUFA4 subunit into complex-IV. Intriguingly, NDUFA4 lies exactly at the dimeric interface observed in previously reported crystal structures of complex-IV homodimer which would preclude complex-IV dimerization. Combining previous structural and biochemical data shown by us and other groups, we propose that the intact complex-IV is a monomer containing 14 subunits.


  • 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 1513Homo sapiensMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
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GTEx:  ENSG00000198804 
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UniProt GroupP00395
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2227Homo sapiensMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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PHAROS:  P00403
GTEx:  ENSG00000198712 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3260Homo sapiensMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
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GTEx:  ENSG00000198938 
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UniProt GroupP00414
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial144Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000131143 
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UniProt GroupP13073
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrial109Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000178741 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial98Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P10606
GTEx:  ENSG00000135940 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A1, mitochondrial75Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000111775 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B182Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000126267 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C73Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000164919 
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UniProt GroupP09669
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A2, mitochondrial56Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000112695 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrial49Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000131174 
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UniProt GroupP24311
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial47Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000127184 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8A, mitochondrial43Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000176340 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit NDUFA479Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000189043 
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
X [auth C]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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Q [auth A],
R [auth A]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEE
Query on PEE

Download Ideal Coordinates CCD File 
S [auth A],
V [auth C],
W [auth C]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
ZN
Query on ZN

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Y [auth F]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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O [auth A],
T [auth B],
U [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
P [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China(973 Program)China2017YFA0504600
National Basic Research Program of China(973 Program)China2016YFA0501100
National Science Foundation (China)China31625008
National Natural Science Foundation of ChinaChina21532004
National Natural Science Foundation of ChinaChina31570733

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release