6YJ4

Structure of Yarrowia lipolytica complex I at 2.7 A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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

Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation.

Grba, D.N.Hirst, J.

(2020) Nat Struct Mol Biol 27: 892-900

  • DOI: https://doi.org/10.1038/s41594-020-0473-x
  • Primary Citation of Related Structures:  
    6YJ4

  • PubMed Abstract: 

    Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-Å-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian 'deactive transition' (relevant to ischemia-reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine.


  • Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3128Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad3YALI1_M00472r
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6C7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q9B6C7 
Go to UniProtKB:  Q9B6C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6C7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)210Yarrowia lipolyticaMutation(s): 0 
Gene Names: nukmYALI1_F09003g
EC: 1.6.99.3
UniProt
Find proteins for Q9UUT7 (Yarrowia lipolytica)
Explore Q9UUT7 
Go to UniProtKB:  Q9UUT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUT7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NUGM protein293Yarrowia lipolyticaMutation(s): 0 
Gene Names: nugmB0I71DRAFT_126141
EC: 1.6.99.3
UniProt
Find proteins for F2Z6D7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore F2Z6D7 
Go to UniProtKB:  F2Z6D7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z6D7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NUCM protein466Yarrowia lipolyticaMutation(s): 0 
Gene Names: nucmB0I71DRAFT_131656YALI1_F22993g
EC: 1.6.99.3
UniProt
Find proteins for F2Z626 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore F2Z626 
Go to UniProtKB:  F2Z626
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z626
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)243Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuhm
EC: 1.6.99.3
UniProt
Find proteins for F2Z6C0 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore F2Z6C0 
Go to UniProtKB:  F2Z6C0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z6C0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)488Yarrowia lipolyticaMutation(s): 0 
Gene Names: nubmNUO51YALI1_B26679g
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for F2Z660 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore F2Z660 
Go to UniProtKB:  F2Z660
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z660
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)728Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuamYALI1_D07089g
EC: 1.6.99.3
UniProt
Find proteins for F2Z6F1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore F2Z6F1 
Go to UniProtKB:  F2Z6F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z6F1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1341Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad1YALI1_M00064g
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6E8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q9B6E8 
Go to UniProtKB:  Q9B6E8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6E8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)229Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuimYALI1_F01456g
EC: 1.6.99.3
UniProt
Find proteins for F2Z619 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore F2Z619 
Go to UniProtKB:  F2Z619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z619
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6185Yarrowia lipolytica CLIB122Mutation(s): 0 
Gene Names: ND6
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6E9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q9B6E9 
Go to UniProtKB:  Q9B6E9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6E9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L89Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad4LYALI1_M00335g
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6D4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q9B6D4 
Go to UniProtKB:  Q9B6D4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6D4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5655Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad5YALI1_M00338r
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6D3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q9B6D3 
Go to UniProtKB:  Q9B6D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6D3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4486Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad4YALI1_M00296g
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6D6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q9B6D6 
Go to UniProtKB:  Q9B6D6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6D6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2469Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad2YALI1_M00458g
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
Find proteins for Q9B6C8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q9B6C8 
Go to UniProtKB:  Q9B6C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9B6C8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)169Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E33570g
Membrane Entity: Yes 
UniProt
Find proteins for Q6C4A6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C4A6 
Go to UniProtKB:  Q6C4A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C4A6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)375Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_137087BD777DRAFT_111096
UniProt
Find proteins for Q6C7X4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C7X4 
Go to UniProtKB:  Q6C7X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C7X4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)161Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_B19507g
Membrane Entity: Yes 
UniProt
Find proteins for Q6CEK9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6CEK9 
Go to UniProtKB:  Q6CEK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CEK9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)136Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_D24109g
UniProt
Find proteins for Q6C8J9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C8J9 
Go to UniProtKB:  Q6C8J9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C8J9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)87Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_C04281g
Membrane Entity: Yes 
UniProt
Find proteins for Q6CD73 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6CD73 
Go to UniProtKB:  Q6CD73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CD73
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)109Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_D18037g
UniProt
Find proteins for Q6C926 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C926 
Go to UniProtKB:  Q6C926
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C926
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)132Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_D32594g
UniProt
Find proteins for Q6C7X2 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C7X2 
Go to UniProtKB:  Q6C7X2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C7X2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)144Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_119420BD777DRAFT_112063
Membrane Entity: Yes 
UniProt
Find proteins for Q6C4W9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C4W9 
Go to UniProtKB:  Q6C4W9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C4W9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)124Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_A01824g
Membrane Entity: Yes 
UniProt
Find proteins for Q6CI60 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6CI60 
Go to UniProtKB:  Q6CI60
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CI60
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)172Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_134276
Membrane Entity: Yes 
UniProt
Find proteins for Q6CGB4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6CGB4 
Go to UniProtKB:  Q6CGB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CGB4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)198Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129038BD777DRAFT_131485
Membrane Entity: Yes 
UniProt
Find proteins for Q6C674 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C674 
Go to UniProtKB:  Q6C674
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C674
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)123Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E34222g
Membrane Entity: Yes 
UniProt
Find proteins for B5FVF8 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5FVF8 
Go to UniProtKB:  B5FVF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5FVF8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)AA [auth a]87Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_C30086g
Membrane Entity: Yes 
UniProt
Find proteins for B5FVD3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5FVD3 
Go to UniProtKB:  B5FVD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5FVD3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)BA [auth b]78Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_131413YALI1_E28107g
Membrane Entity: Yes 
UniProt
Find proteins for B5FVF3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5FVF3 
Go to UniProtKB:  B5FVF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5FVF3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)CA [auth c]182Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129288YALI1_A03153g
UniProt
Find proteins for Q6CI10 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6CI10 
Go to UniProtKB:  Q6CI10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CI10
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)DA [auth d]74Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E00527g
UniProt
Find proteins for A0A1D8NGI5 (Yarrowia lipolytica)
Explore A0A1D8NGI5 
Go to UniProtKB:  A0A1D8NGI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D8NGI5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)EA [auth e]89Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_F24343g
Membrane Entity: Yes 
UniProt
Find proteins for B5RSL7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5RSL7 
Go to UniProtKB:  B5RSL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5RSL7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)FA [auth f]138Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_100046YALI1_B00908g
Membrane Entity: Yes 
UniProt
Find proteins for Q6CG53 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6CG53 
Go to UniProtKB:  Q6CG53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CG53
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)GA [auth g]249Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuwmB0I71DRAFT_98177YALI1_E34367g
EC: 1.6.99.3
UniProt
Find proteins for F2Z673 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore F2Z673 
Go to UniProtKB:  F2Z673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z673
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)HA [auth h]139Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_126580
UniProt
Find proteins for Q6C1R9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C1R9 
Go to UniProtKB:  Q6C1R9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C1R9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)IA [auth i]90Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_133979YALI1_D22691g
Membrane Entity: Yes 
UniProt
Find proteins for A0A1H6Q311 (Yarrowia lipolytica)
Explore A0A1H6Q311 
Go to UniProtKB:  A0A1H6Q311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1H6Q311
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
subunit NIGM of protein NADH:Ubiquinone Oxidoreductase (Complex I)JA [auth j]91Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129560YALI1_D30003g
UniProt
Find proteins for A0A1D8NFX6 (Yarrowia lipolytica)
Explore A0A1D8NFX6 
Go to UniProtKB:  A0A1D8NFX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D8NFX6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)KA [auth k]60Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_135324
Membrane Entity: Yes 
UniProt
Find proteins for B5FVE5 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5FVE5 
Go to UniProtKB:  B5FVE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5FVE5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)LA [auth l]149Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_129122YALI1_D06302g
Membrane Entity: Yes 
UniProt
Find proteins for Q6CA88 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6CA88 
Go to UniProtKB:  Q6CA88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CA88
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)MA [auth m]93Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuvmYALI1_F09017g
EC: 1.6.99.3
Membrane Entity: Yes 
UniProt
Find proteins for B5RSK9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5RSK9 
Go to UniProtKB:  B5RSK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5RSK9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)NA [auth n]109Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_D09203g
Membrane Entity: Yes 
UniProt
Find proteins for Q6C9Z1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C9Z1 
Go to UniProtKB:  Q6C9Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C9Z1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)OA [auth o]99Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E37603g
Membrane Entity: Yes 
UniProt
Find proteins for B5FVG1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5FVG1 
Go to UniProtKB:  B5FVG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5FVG1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)PA [auth p]92Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_A18188g
Membrane Entity: Yes 
UniProt
Find proteins for B5RSK3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore B5RSK3 
Go to UniProtKB:  B5RSK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5RSK3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
EC [auth Z]
HC [auth a]
IC [auth b]
NB [auth M]
TB [auth O]
EC [auth Z],
HC [auth a],
IC [auth b],
NB [auth M],
TB [auth O],
WB [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
CB [auth H]
CC [auth Y]
DB [auth I]
FC [auth Z]
GC [auth Z]
CB [auth H],
CC [auth Y],
DB [auth I],
FC [auth Z],
GC [auth Z],
IB [auth L],
JB [auth L],
JC [auth b],
KB [auth L],
KC [auth b],
LB [auth L],
LC [auth d],
NC [auth d],
OB [auth M],
QA [auth A],
QB [auth M],
RA [auth A],
SB [auth N]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP

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

Download Ideal Coordinates CCD File 
BB [auth H]
GB [auth L]
HB [auth L]
MB [auth L]
MC [auth d]
BB [auth H],
GB [auth L],
HB [auth L],
MB [auth L],
MC [auth d],
RB [auth N],
UA [auth D],
UB [auth P]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
EHZ
Query on EHZ

Download Ideal Coordinates CCD File 
YB [auth T],
ZB [auth U]
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
AC [auth Y],
BC [auth Y],
DC [auth Y],
PB [auth M],
TA [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
WA [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
EB [auth I]
FB [auth I]
SA [auth B]
XA [auth F]
YA [auth G]
EB [auth I],
FB [auth I],
SA [auth B],
XA [auth F],
YA [auth G],
ZA [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
AB [auth G],
VA [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
XB [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET
2MR
Query on 2MR
D
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.14
MODEL REFINEMENTPHENIX1.16

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105663141
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2021-02-10
    Changes: Database references
  • Version 1.4: 2021-03-17
    Changes: Database references