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 1.4 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. 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: 

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
75-KDA PROTEIN (NUAM)728Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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UniProt GroupQ9UUU3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
51-KDA PROTEIN (NUBM)488Yarrowia lipolyticaMutation(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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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
49-KDA PROTEIN (NUCM)466Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NIMM SUBUNIT87Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NUEM SUBUNIT375Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NUFM SUBUNIT144Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30-KDA PROTEIN (NUGM)281Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
24-KDA SUBUNIT (NUHM)243Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
TYKY SUBUNIT (NUIM)229Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NUJM SUBUNIT198Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PSST SUBUNIT (NUKM)210Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ND4L SUBUNIT (NULM)86Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NUMM SUBUNIT136Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ACPM1 SUBUNITN [auth O]109Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NB4M SUBUNITO [auth P]124Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ACPM2 SUBUNITP [auth Q]132Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NI2M SUBUNITQ [auth R]109Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NESM SUBUNITR [auth S]159Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NUPM SUBUNITS [auth U]172Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NB6M SUBUNITT [auth W]123Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NUXM SUBUNITU [auth X]169Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NUYM SUBUNITV [auth Y]161Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NUZM SUBUNITW [auth Z]137Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NIAM SUBUNITX [auth a]100Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NEBM SUBUNITY [auth b]64Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NB2M SUBUNITZ [auth c]60Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NIDM SUBUNITAA [auth d]92Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NUUM SUBUNITBA [auth e]45Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NI8M SUBUNITCA [auth f]87Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NI9M SUBUNITDA [auth g]63Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
N7BM SUBUNITEA [auth h]138Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
UNKNOWN SUBUNITFA [auth i]53Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NB5M SUBUNITGA [auth j]93Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
Membrane Entity: Yes 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NUNM SUBUNITHA [auth n]93Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 35
MoleculeChains Sequence 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 
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Entity ID: 36
MoleculeChains Sequence 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 
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Entity ID: 37
MoleculeChains Sequence 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 
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Entity ID: 38
MoleculeChains Sequence 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 
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Entity ID: 39
MoleculeChains Sequence 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 
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Entity ID: 40
MoleculeChains Sequence 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 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NB8M SUBUNITOA [auth 8]99Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NIPM SUBUNITPA [auth 9]89Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
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CB [auth g]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PE
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DB [auth g],
EB [auth 1],
FB [auth 4]		1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP
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VA [auth E]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
ZMP
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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
FMN
Query on FMN
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UA [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4
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QA [auth A]
RA [auth A]
TA [auth B]
XA [auth I]
YA [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES
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SA [auth A],
WA [auth H]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN
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AB [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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



View more in-depth experimental data
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
  • Version 1.4: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary