6RFQ

Cryo-EM structure of a respiratory complex I assembly intermediate with NDUFAF2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.

Parey, K., Haapanen, O., Sharma, V., Kofeler, H., Zullig, T., Prinz, S., Siegmund, K., Wittig, I., Mills, D.J., Vonck, J., Kuhlbrandt, W., Zickermann, V.

(2019) Sci Adv 5: eaax9484-eaax9484

  • DOI: https://doi.org/10.1126/sciadv.aax9484
  • Primary Citation of Related Structures:  
    6RFQ, 6RFR, 6RFS

  • PubMed Abstract: 

    Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast Yarrowia lipolytica by electron cryo-microscopy at 3.2-Å resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane.

    • Organizational Affiliation: 

    Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)728Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
Find proteins for F2Z6F1 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)488Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (PDB Primary Data)
UniProt
Find proteins for F2Z660 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)466Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
Find proteins for F2Z626 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)87Yarrowia lipolyticaMutation(s): 0 
UniProt
Find proteins for B5FVD3 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)375Yarrowia lipolyticaMutation(s): 0 
UniProt
Find proteins for Q6C7X4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)144Yarrowia lipolyticaMutation(s): 0 
UniProt
Find proteins for Q6C4W9 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)281Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
Find proteins for F2Z6D7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)243Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)229Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)198Yarrowia lipolyticaMutation(s): 0 
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Find proteins for Q6C674 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)210Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)89Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)M [auth O]109Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)N [auth P]124Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)O [auth Q]132Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)P [auth R]109Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)Q [auth S]249Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
UniProt
Find proteins for F2Z673 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)R [auth U]172Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q6CGB4 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)S [auth W]123Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)T [auth X]169Yarrowia lipolyticaMutation(s): 0 
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Find proteins for Q6C4A6 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)U [auth Y]161Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)V [auth Z]182Yarrowia lipolyticaMutation(s): 0 
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Find proteins for Q6CI10 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)W [auth a]149Yarrowia lipolyticaMutation(s): 0 
UniProt
Find proteins for Q6CA88 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)X [auth b]74Yarrowia lipolyticaMutation(s): 0 
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Find proteins for A0A1D8NGI5 (Yarrowia lipolytica)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)Y [auth c]60Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)Z [auth d]92Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)AA [auth e]67Yarrowia lipolyticaMutation(s): 0 
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Find proteins for A0A1D8NFX6 (Yarrowia lipolytica)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)BA [auth f]87Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)CA [auth g]78Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)DA [auth i]90Yarrowia lipolyticaMutation(s): 0 
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Find proteins for A0A1H6Q311 (Yarrowia lipolytica)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)EA [auth j]93Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.99.3
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit N7BML assembly factorFA [auth k]237Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)GA [auth n]120Yarrowia lipolyticaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)HA [auth 1]341Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)IA [auth 2]469Yarrowia lipolyticaMutation(s): 0 
EC: 1.6.5.3
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)JA [auth 3]128Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)KA [auth 4]486Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)LA [auth 5]655Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)MA [auth 6]185Yarrowia lipolyticaMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)NA [auth 8]99Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)OA [auth 9]89Yarrowia lipolyticaMutation(s): 0 
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL
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CB [auth J],
IB [auth X],
JB [auth g],
RB [auth 4]		CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LMN
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AB [auth J],
LB [auth j]		Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
T7X
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NB [auth 2],
PB [auth 2],
TB [auth 4]		Phosphatidylinositol
C47 H83 O13 P
KRTOMQDUKGRFDJ-TWUHCGEESA-N
CPL
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OB [auth 2]1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
3PE
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BB [auth J]
KB [auth g]
QB [auth 4]
SB [auth 4]
UB [auth 4]
BB [auth J],
KB [auth g],
QB [auth 4],
SB [auth 4],
UB [auth 4],
VB [auth 5],
XB [auth 5],
YA [auth I],
YB [auth 6],
ZA [auth J]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
Query on NDP
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UA [auth E]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PLC
Query on PLC
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GB [auth W],
HB [auth W],
MB [auth n],
WB [auth 5]		DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
ZMP
Query on ZMP
Download Ideal Coordinates CCD File 
EB [auth O],
FB [auth Q]		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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TA [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4
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DB [auth K]
PA [auth A]
QA [auth A]
SA [auth B]
WA [auth I]
DB [auth K],
PA [auth A],
QA [auth A],
SA [auth B],
WA [auth I],
XA [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES
Download Ideal Coordinates CCD File 
RA [auth A],
VA [auth H]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

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: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2021-06-02
    Changes: Derived calculations
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary