9TI4 | pdb_00009ti4

High resolution Cryo-EM structure of human complex I in mitochondria


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 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

Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome

Nguyen, M.D.Singh, V.Rorbach, J.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialA [auth C]434Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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PHAROS:  P49821
GTEx:  ENSG00000167792 
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UniProt GroupP49821
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialB [auth D]176Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for O00217 (Homo sapiens)
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PHAROS:  O00217
GTEx:  ENSG00000110717 
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UniProt GroupO00217
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialC [auth E]161Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for O75251 (Homo sapiens)
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GTEx:  ENSG00000115286 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6D [auth F]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000184983 
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UniProt GroupP56556
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2E [auth G]85Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131495 
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UniProt GroupO43678
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialF [auth H],
U [auth X]
86Homo sapiensMutation(s): 0 
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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 I]112Homo sapiensMutation(s): 0 
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Find proteins for Q16718 (Homo sapiens)
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GTEx:  ENSG00000128609 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialH [auth J]341Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139180 
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UniProt GroupQ16795
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialI [auth K]39Homo sapiensMutation(s): 0 
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Find proteins for P56181 (Homo sapiens)
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GTEx:  ENSG00000160194 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialJ [auth L]121Homo sapiensMutation(s): 0 
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Find proteins for O43181 (Homo sapiens)
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GTEx:  ENSG00000164258 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialK [auth M]687Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P28331 (Homo sapiens)
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GTEx:  ENSG00000023228 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12L [auth N]144Homo sapiensMutation(s): 0 
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Find proteins for Q9UI09 (Homo sapiens)
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PHAROS:  Q9UI09
GTEx:  ENSG00000184752 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialM [auth O]212Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P19404 (Homo sapiens)
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GTEx:  ENSG00000178127 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialN [auth P]208Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for O75489 (Homo sapiens)
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GTEx:  ENSG00000213619 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialO [auth Q]430Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for O75306 (Homo sapiens)
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GTEx:  ENSG00000158864 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1P [auth S]70Homo sapiensMutation(s): 0 
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Find proteins for O15239 (Homo sapiens)
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PHAROS:  O15239
GTEx:  ENSG00000125356 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialQ [auth T]96Homo sapiensMutation(s): 0 
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Find proteins for O75380 (Homo sapiens)
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GTEx:  ENSG00000145494 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3R [auth U]83Homo sapiensMutation(s): 0 
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Find proteins for O95167 (Homo sapiens)
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PHAROS:  O95167
GTEx:  ENSG00000170906 
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UniProt GroupO95167
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11S [auth V]140Homo sapiensMutation(s): 0 
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Find proteins for Q86Y39 (Homo sapiens)
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PHAROS:  Q86Y39
GTEx:  ENSG00000174886 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13T [auth W]140Homo sapiensMutation(s): 0 
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Find proteins for Q9P0J0 (Homo sapiens)
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GTEx:  ENSG00000186010 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialV [auth Y]61Homo sapiensMutation(s): 0 
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Find proteins for O95178 (Homo sapiens)
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GTEx:  ENSG00000090266 
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UniProt GroupO95178
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3W [auth Z]83Homo sapiensMutation(s): 0 
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Find proteins for O43676 (Homo sapiens)
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PHAROS:  O43676
GTEx:  ENSG00000119013 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialX [auth a]138Homo sapiensMutation(s): 0 
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Find proteins for O43674 (Homo sapiens)
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GTEx:  ENSG00000136521 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6Y [auth b]120Homo sapiensMutation(s): 0 
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Find proteins for O95139 (Homo sapiens)
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GTEx:  ENSG00000165264 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialZ [auth c]152Homo sapiensMutation(s): 0 
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Find proteins for O95169 (Homo sapiens)
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GTEx:  ENSG00000166136 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10AA [auth d]169Homo sapiensMutation(s): 0 
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Find proteins for O96000 (Homo sapiens)
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PHAROS:  O96000
GTEx:  ENSG00000140990 
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UniProt GroupO96000
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialBA [auth e]107Homo sapiensMutation(s): 0 
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Find proteins for Q9NX14 (Homo sapiens)
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PHAROS:  Q9NX14
GTEx:  ENSG00000147123 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialCA [auth f]49Homo sapiensMutation(s): 0 
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Find proteins for O43677 (Homo sapiens)
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PHAROS:  O43677
GTEx:  ENSG00000109390 
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UniProt GroupO43677
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2DA [auth g]119Homo sapiensMutation(s): 0 
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Find proteins for O95298 (Homo sapiens)
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GTEx:  ENSG00000151366 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5EA [auth h]105Homo sapiensMutation(s): 0 
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Find proteins for O43920 (Homo sapiens)
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PHAROS:  O43920
GTEx:  ENSG00000168653 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2FA [auth i]347Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03891 (Homo sapiens)
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GTEx:  ENSG00000198763 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3GA [auth j]115Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03897 (Homo sapiens)
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GTEx:  ENSG00000198840 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LHA [auth k]98Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03901 (Homo sapiens)
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GTEx:  ENSG00000212907 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5IA [auth l]601Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03915 (Homo sapiens)
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PHAROS:  P03915
GTEx:  ENSG00000198786 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6JA [auth m]173Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03923 (Homo sapiens)
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PHAROS:  P03923
GTEx:  ENSG00000198695 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1KA [auth n]54Homo sapiensMutation(s): 0 
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Find proteins for O75438 (Homo sapiens)
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PHAROS:  O75438
GTEx:  ENSG00000183648 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4LA [auth o]128Homo sapiensMutation(s): 0 
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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: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9MA [auth p]173Homo sapiensMutation(s): 0 
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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: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4NA [auth r]459Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03905 (Homo sapiens)
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PHAROS:  P03905
GTEx:  ENSG00000198886 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1OA [auth s]316Homo sapiensMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03886 (Homo sapiens)
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Go to UniProtKB:  P03886
PHAROS:  P03886
GTEx:  ENSG00000198888 
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UniProt GroupP03886
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8PA [auth u]171Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7QA [auth v]121Homo sapiensMutation(s): 0 
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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: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialRA [auth w]320Homo sapiensMutation(s): 0 
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Find proteins for O95299 (Homo sapiens)
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PHAROS:  O95299
GTEx:  ENSG00000130414 
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UniProt GroupO95299
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7SA [auth t]113Homo sapiensMutation(s): 0 
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Find proteins for O95182 (Homo sapiens)
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PHAROS:  O95182
GTEx:  ENSG00000267855 
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UniProt GroupO95182
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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JB [auth V]
KB [auth V]
PB [auth i]
UB [auth l]
VB [auth l]
JB [auth V],
KB [auth V],
PB [auth i],
UB [auth l],
VB [auth l],
ZB [auth u]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PLX
Query on PLX

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FB [auth N]
NB [auth g]
OB [auth g]
SB [auth j]
WB [auth o]
FB [auth N],
NB [auth g],
OB [auth g],
SB [auth j],
WB [auth o],
XB [auth r],
YB [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
NDP (Subject of Investigation/LOI)
Query on NDP

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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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BB [auth J]
IB [auth V]
LB [auth W]
QB [auth i]
RB [auth i]
BB [auth J],
IB [auth V],
LB [auth W],
QB [auth i],
RB [auth i],
TB [auth l],
XA [auth E]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
8Q1 (Subject of Investigation/LOI)
Query on 8Q1

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MB [auth X],
ZA [auth F]
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
DGT (Subject of Investigation/LOI)
Query on DGT

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AC [auth w]2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

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

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CB [auth M]
DB [auth M]
TA [auth C]
VA [auth D]
WA [auth D]
CB [auth M],
DB [auth M],
TA [auth C],
VA [auth D],
WA [auth D],
YA [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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EB [auth M],
GB [auth O]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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HB [auth T]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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BC [auth w]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
C [auth E]L-PEPTIDE LINKINGC3 H8 N O6 PSER
NMM
Query on NMM
O [auth Q]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release