6GCS

Cryo-EM structure of respiratory complex I from Yarrowia lipolytica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.32 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

Cryo-EM structure of respiratory complex I at work.

Parey, K.Brandt, U.Xie, H.Mills, D.J.Siegmund, K.Vonck, J.Kuehlbrandt, W.Zickermann, V.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.39213
  • Primary Citation of Related Structures:  
    6GCS

  • PubMed Abstract: 
  • Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm ...

    Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast Yarrowia lipolytica both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.


    Organizational Affiliation

    Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
75-KDA PROTEIN (NUAM)728Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuamB0I71DRAFT_14167YALI1_D07089g
EC: 1.6.99.3
UniProt
Find proteins for Q9UUU3 (Yarrowia lipolytica)
Explore Q9UUU3 
Go to UniProtKB:  Q9UUU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUU3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
51-KDA PROTEIN (NUBM)488Yarrowia lipolyticaMutation(s): 0 
Gene Names: nubmNUO51YALI1_B26679g
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q9UUU2 (Yarrowia lipolytica)
Explore Q9UUU2 
Go to UniProtKB:  Q9UUU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUU2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
49-KDA PROTEIN (NUCM)466Yarrowia lipolyticaMutation(s): 0 
Gene Names: nucmB0I71DRAFT_131656YALI1_F22993g
EC: 1.6.99.3
UniProt
Find proteins for Q9UUU1 (Yarrowia lipolytica)
Explore Q9UUU1 
Go to UniProtKB:  Q9UUU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUU1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NIMM SUBUNIT87Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NUEM SUBUNIT375Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NUFM SUBUNIT144Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30-KDA PROTEIN (NUGM)281Yarrowia lipolyticaMutation(s): 0 
Gene Names: nugmB0I71DRAFT_126141
EC: 1.6.99.3
UniProt
Find proteins for Q9UUU0 (Yarrowia lipolytica)
Explore Q9UUU0 
Go to UniProtKB:  Q9UUU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUU0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
24-KDA SUBUNIT (NUHM)243Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuhmB0I71DRAFT_136742
EC: 1.6.99.3
UniProt
Find proteins for Q9UUT9 (Yarrowia lipolytica)
Explore Q9UUT9 
Go to UniProtKB:  Q9UUT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUT9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
TYKY SUBUNIT (NUIM)229Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuimB0I71DRAFT_132693YALI1_F01456g
EC: 1.6.99.3
UniProt
Find proteins for Q9UUT8 (Yarrowia lipolytica)
Explore Q9UUT8 
Go to UniProtKB:  Q9UUT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UUT8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NUJM SUBUNIT198Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
PSST SUBUNIT (NUKM)210Yarrowia lipolyticaMutation(s): 0 
Gene Names: nukmB0I71DRAFT_136033YALI1_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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
ND4L SUBUNIT (NULM)86Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NUMM SUBUNIT136Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ACPM1 SUBUNITN [auth O]109Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NB4M SUBUNITO [auth P]124Yarrowia lipolyticaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ACPM2 SUBUNITP [auth Q]132Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NI2M SUBUNITQ [auth R]109Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NESM SUBUNITR [auth S]159Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
NUPM SUBUNITS [auth U]172Yarrowia lipolyticaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
NB6M SUBUNITT [auth W]123Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
NUXM SUBUNITU [auth X]169Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
NUYM SUBUNITV [auth Y]161Yarrowia lipolyticaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
NUZM SUBUNITW [auth Z]137Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
NIAM SUBUNITX [auth a]100Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
NEBM SUBUNITY [auth b]64Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
NB2M SUBUNITZ [auth c]60Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
NIDM SUBUNITAA [auth d]92Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
NUUM SUBUNITBA [auth e]45Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
NI8M SUBUNITCA [auth f]87Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NI9M SUBUNITDA [auth g]63Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
N7BM SUBUNITEA [auth h]138Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
UNKNOWN SUBUNITFA [auth i]53Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
NB5M SUBUNITGA [auth j]93Yarrowia lipolyticaMutation(s): 0 
Gene Names: nuvmB0I71DRAFT_136036YALI1_F09017g
EC: 1.6.99.3
Membrane Entity: Yes 
UniProt
Find proteins for Q6ZY24 (Yarrowia lipolytica)
Explore Q6ZY24 
Go to UniProtKB:  Q6ZY24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZY24
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
NUNM SUBUNITHA [auth n]93Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
ND1 SUBUNIT (NU1M)IA [auth 1]341Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
ND2 SUBUNIT (NU2M)JA [auth 2]469Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
ND3 SUBUNIT (NU3M)KA [auth 3]128Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
ND4 SUBUNIT (NU4M)LA [auth 4]486Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
ND5 SUBUNIT (NU5M)MA [auth 5]655Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
ND6 SUBUNIT (NU6M)NA [auth 6]185Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
NB8M SUBUNITOA [auth 8]99Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
NIPM SUBUNITPA [auth 9]89Yarrowia lipolyticaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
CB [auth g]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
DB [auth g],
EB [auth 1],
FB [auth 4]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
NDP
Query on NDP

Download Ideal Coordinates CCD File 
VA [auth E]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
ZMP
Query on ZMP

Download Ideal Coordinates CCD File 
BB [auth O]S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
C25 H49 N2 O8 P S
HDTINWYIVVMRIN-HSZRJFAPSA-N
 Ligand Interaction
FMN
Query on FMN

Download Ideal Coordinates CCD File 
UA [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
QA [auth A]
RA [auth A]
TA [auth B]
XA [auth I]
YA [auth I]
QA [auth A],
RA [auth A],
TA [auth B],
XA [auth I],
YA [auth I],
ZA [auth K]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
SA [auth A],
WA [auth H]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.12_2829

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEXC 115

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-12-11
    Changes: Other
  • Version 1.3: 2021-06-02
    Changes: Derived calculations