7ZKQ

Early Pp module assembly intermediate of complex I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling.

Schiller, J.Laube, E.Wittig, I.Kuhlbrandt, W.Vonck, J.Zickermann, V.

(2022) Sci Adv 8: eadd3855-eadd3855

  • DOI: 10.1126/sciadv.add3855
  • Primary Citation of Related Structures:  
    7ZKP, 7ZKQ

  • PubMed Abstract: 
  • Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system ...

    Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation.


    Organizational Affiliation

    Center for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2A [auth 2]469Yarrowia lipolyticaMutation(s): 0 
Gene Names: nad2YALI1_M00458g
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
Find proteins for S5U4R9 (Yarrowia lipolytica)
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UniProt GroupS5U4R9
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)B [auth b]74Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_E00527g
UniProt
Find proteins for A0A1D8NGI5 (Yarrowia lipolytica)
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UniProt GroupA0A1D8NGI5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Complex I intermediate-associated protein 30-domain-containing proteinC [auth A]284Yarrowia lipolyticaMutation(s): 0 
Gene Names: B0I71DRAFT_38716
UniProt
Find proteins for A0A371C5R6 (Yarrowia lipolytica)
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UniProt GroupA0A371C5R6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
complex I assembly factor CIA84D [auth C]852Yarrowia lipolyticaMutation(s): 0 
Gene Names: YALI1_B02228g
UniProt
Find proteins for A0A1D8N612 (Yarrowia lipolytica)
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UniProt GroupA0A1D8N612
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Tafazzin family proteinE [auth T]372Yarrowia lipolyticaMutation(s): 0 
UniProt
Find proteins for Q6CBZ7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
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UniProt GroupQ6CBZ7
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
F [auth b],
I [auth T]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
LMN
Query on LMN

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G [auth C]Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
 Ligand Interaction
PLC
Query on PLC

Download Ideal Coordinates CCD File 
H [auth T]DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A [auth 2]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyZI 552/4-2

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Data collection, Database references, Structure summary