5XTC

Cryo-EM structure of human respiratory complex I transmembrane arm

  • Classification: 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 1.3 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] iron-sulfur protein 2, mitochondrialA [auth Q]46Homo sapiensMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O75306 (Homo sapiens)
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PHAROS:  O75306
GTEx:  ENSG00000158864 
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UniProt GroupO75306
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1B [auth S]70Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O15239 (Homo sapiens)
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PHAROS:  O15239
GTEx:  ENSG00000125356 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3C [auth U]83Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000170906 
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UniProt GroupO95167
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11D [auth V]140Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000174886 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13E [auth W]116Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000186010 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialF [auth X]85Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O14561 (Homo sapiens)
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PHAROS:  O14561
GTEx:  ENSG00000004779 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialG [auth Y]59Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000090266 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3H [auth Z]80Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  O43676
GTEx:  ENSG00000119013 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialI [auth a]138Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000136521 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6J [auth b]128Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O95139 (Homo sapiens)
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GTEx:  ENSG00000165264 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialK [auth c]153Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000166136 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10L [auth d]171Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O96000 (Homo sapiens)
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PHAROS:  O96000
GTEx:  ENSG00000140990 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialM [auth e]97Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000147123 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialN [auth f]47Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000109390 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2O [auth g]119Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O95298 (Homo sapiens)
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GTEx:  ENSG00000151366 
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UniProt GroupO95298
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5P [auth h]104Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O43920 (Homo sapiens)
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PHAROS:  O43920
GTEx:  ENSG00000168653 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2Q [auth i]347Homo sapiensMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Find proteins for P03891 (Homo sapiens)
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PHAROS:  P03891
GTEx:  ENSG00000198763 
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UniProt GroupP03891
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3R [auth j]115Homo sapiensMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Find proteins for P03897 (Homo sapiens)
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PHAROS:  P03897
GTEx:  ENSG00000198840 
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UniProt GroupP03897
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LS [auth k]97Homo sapiensMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Find proteins for P03901 (Homo sapiens)
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GTEx:  ENSG00000212907 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5T [auth l]603Homo sapiensMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Find proteins for P03915 (Homo sapiens)
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GTEx:  ENSG00000198786 
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UniProt GroupP03915
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6U [auth m]174Homo sapiensMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Find proteins for P03923 (Homo sapiens)
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GTEx:  ENSG00000198695 
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UniProt GroupP03923
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1V [auth n]56Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O75438 (Homo sapiens)
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GTEx:  ENSG00000183648 
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UniProt GroupO75438
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4W [auth o]128Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O95168 (Homo sapiens)
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GTEx:  ENSG00000065518 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9X [auth p]172Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000147684 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4Y [auth r]459Homo sapiensMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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GTEx:  ENSG00000198886 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1Z [auth s]318Homo sapiensMutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
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Find proteins for P03886 (Homo sapiens)
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GTEx:  ENSG00000198888 
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UniProt GroupP03886
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8AA [auth u]169Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P51970 (Homo sapiens)
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GTEx:  ENSG00000119421 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7BA [auth v]122Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000099795 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialCA [auth w]320Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000130414 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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EA [auth V],
MA [auth i],
PA [auth l],
QA [auth l],
RA [auth n]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PLX
Query on PLX

Download Ideal Coordinates CCD File 
DA [auth U]
GA [auth V]
IA [auth b]
JA [auth g]
KA [auth g]
DA [auth U],
GA [auth V],
IA [auth b],
JA [auth g],
KA [auth g],
LA [auth g],
TA [auth r],
UA [auth r],
VA [auth s]
(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
PEE
Query on PEE

Download Ideal Coordinates CCD File 
FA [auth V],
HA [auth W],
NA [auth l],
OA [auth l]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
8Q1
Query on 8Q1

Download Ideal Coordinates CCD File 
SA [auth p]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
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