5XTD

Cryo-EM structure of human respiratory complex I

  • Classification: OXIDOREDUCTASE/ELECTRON TRANSPORT
  • Organism(s): Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTM

  • Deposited: 2017-06-19 Released: 2017-08-30 
  • Deposition Author(s): Gu, J., Wu, M., Yang, M.
  • Funding Organization(s): Ministry of Science and Technology, National Science Fund for Distinguished Young Scholars, National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.

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

(2017) Cell 170: 1247-1257.e12

  • DOI: https://doi.org/10.1016/j.cell.2017.07.050
  • Primary Citation of Related Structures:  
    5XTB, 5XTC, 5XTD, 5XTE, 5XTH, 5XTI

  • PubMed Abstract: 

    The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-I 2 III 2 IV 2 (MCI 2 III 2 IV 2 ) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCI 2 III 2 IV 2 forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c 1 state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole.


  • 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, 100084 Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial431Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for P49821 (Homo sapiens)
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PHAROS:  P49821
GTEx:  ENSG00000167792 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial176Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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GTEx:  ENSG00000110717 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial156Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for O75251 (Homo sapiens)
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GTEx:  ENSG00000115286 
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UniProt GroupO75251
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6D [auth E]113Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000184983 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2E [auth F]83Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000131495 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialF [auth G],
V [auth X]
85Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000004779 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5G [auth H]112Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000128609 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7H [auth I]110Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000267855 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialI [auth J]337Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000139180 
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UniProt GroupQ16795
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialJ [auth K]33Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000160194 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialK [auth L]118Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000164258 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialL [auth M]687Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for P28331 (Homo sapiens)
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GTEx:  ENSG00000023228 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12M [auth N]143Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000184752 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialN [auth O]212Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for P19404 (Homo sapiens)
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GTEx:  ENSG00000178127 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialO [auth P]208Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for O75489 (Homo sapiens)
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GTEx:  ENSG00000213619 
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UniProt GroupO75489
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialP [auth Q]430Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for O75306 (Homo sapiens)
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GTEx:  ENSG00000158864 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1Q [auth S]70Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O15239 (Homo sapiens)
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GTEx:  ENSG00000125356 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialR [auth T]95Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O75380 (Homo sapiens)
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GTEx:  ENSG00000145494 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3S [auth U]83Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000170906 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11T [auth V]140Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000174886 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13U [auth W]138Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9P0J0 (Homo sapiens)
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GTEx:  ENSG00000186010 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialW [auth Y]59Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000090266 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3X [auth Z]80Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000119013 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialY [auth a]138Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000136521 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6Z [auth b]128Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000165264 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialAA [auth c]153Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000166136 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10BA [auth d]171Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000140990 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialCA [auth e]97Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000147123 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialDA [auth f]47Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000109390 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2EA [auth g]119Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000151366 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5FA [auth h]104Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000168653 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2GA [auth i]347Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for P03891 (Homo sapiens)
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GTEx:  ENSG00000198763 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3HA [auth j]115Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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GTEx:  ENSG00000198840 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LIA [auth k]97Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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GTEx:  ENSG00000212907 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5JA [auth l]603Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for P03915 (Homo sapiens)
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PHAROS:  P03915
GTEx:  ENSG00000198786 
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UniProt GroupP03915
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6KA [auth m]174Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for P03923 (Homo sapiens)
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PHAROS:  P03923
GTEx:  ENSG00000198695 
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UniProt GroupP03923
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1LA [auth n]56Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O75438 (Homo sapiens)
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PHAROS:  O75438
GTEx:  ENSG00000183648 
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UniProt GroupO75438
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth o]128Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O95168 (Homo sapiens)
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PHAROS:  O95168
GTEx:  ENSG00000065518 
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UniProt GroupO95168
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9NA [auth p]172Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9Y6M9 (Homo sapiens)
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PHAROS:  Q9Y6M9
GTEx:  ENSG00000147684 
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UniProt GroupQ9Y6M9
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4OA [auth r]459Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for P03905 (Homo sapiens)
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PHAROS:  P03905
GTEx:  ENSG00000198886 
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UniProt GroupP03905
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1PA [auth s]318Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Find proteins for P03886 (Homo sapiens)
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PHAROS:  P03886
GTEx:  ENSG00000198888 
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UniProt GroupP03886
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8QA [auth u]169Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P51970 (Homo sapiens)
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PHAROS:  P51970
GTEx:  ENSG00000119421 
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UniProt GroupP51970
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7RA [auth v]137Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P17568 (Homo sapiens)
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PHAROS:  P17568
GTEx:  ENSG00000099795 
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UniProt GroupP17568
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialSA [auth w]320Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O95299 (Homo sapiens)
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PHAROS:  O95299
GTEx:  ENSG00000130414 
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
GB [auth V],
OB [auth i],
RB [auth l],
SB [auth l],
TB [auth n]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PLX
Query on PLX

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FB [auth U]
IB [auth V]
KB [auth b]
LB [auth g]
MB [auth g]
FB [auth U],
IB [auth V],
KB [auth b],
LB [auth g],
MB [auth g],
NB [auth g],
VB [auth r],
WB [auth r],
XA [auth B]
(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

Download Ideal Coordinates CCD File 
AB [auth J]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PEE
Query on PEE

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HB [auth V],
JB [auth W],
PB [auth l],
QB [auth l]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
8Q1
Query on 8Q1

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UB [auth p],
ZA [auth E]
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
FMN
Query on FMN

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

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BB [auth M]
CB [auth M]
TA [auth A]
VA [auth B]
WA [auth B]
BB [auth M],
CB [auth M],
TA [auth A],
VA [auth B],
WA [auth B],
YA [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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DB [auth M],
EB [auth O]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.11.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyChina2016YFA0501100
Ministry of Science and TechnologyChina2017YFA0504600
National Science Fund for Distinguished Young ScholarsChina31625008
National Natural Science Foundation of ChinaChina21532004
National Natural Science Foundation of ChinaChina31570733

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Data processing, Database references
  • Version 1.3: 2019-11-06
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.4: 2019-11-20
    Changes: Advisory, Derived calculations