8QC1 | pdb_00008qc1

Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the turnover-ready state of an ancestral respiratory complex I.

Ivanov, B.S.Bridges, H.R.Jarman, O.D.Hirst, J.

(2024) Nat Commun 15: 9340-9340

  • DOI: https://doi.org/10.1038/s41467-024-53679-3
  • Primary Citation of Related Structures:  
    8QBY, 8QC1

  • PubMed Abstract: 

    Respiratory complex I is pivotal for cellular energy conversion, harnessing energy from NADH:ubiquinone oxidoreduction to drive protons across energy-transducing membranes for ATP synthesis. Despite detailed structural information on complex I, its mechanism of catalysis remains elusive due to lack of accompanying functional data for comprehensive structure-function analyses. Here, we present the 2.3-Å resolution structure of complex I from the α-proteobacterium Paracoccus denitrificans, a close relative of the mitochondrial progenitor, in phospholipid-bilayer nanodiscs. Three eukaryotic-type supernumerary subunits (NDUFS4, NDUFS6 and NDUFA12) plus a novel L-isoaspartyl-O-methyltransferase are bound to the core complex. Importantly, the enzyme is in a single, homogeneous resting state that matches the closed, turnover-ready (active) state of mammalian complex I. Our structure reveals the elements that stabilise the closed state and completes P. denitrificans complex I as a unified platform for combining structure, function and genetics in mechanistic studies.


  • Organizational Affiliation
    • The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit MA [auth M]513Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
Find proteins for A1B480 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B480 
Go to UniProtKB:  A1B480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1B480
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit LB [auth L]703Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
Find proteins for A1B481 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B481 
Go to UniProtKB:  A1B481
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1B481
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
J [auth M]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
P5S
Query on P5S

Download Ideal Coordinates CCD File 
O [auth L]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
F [auth M],
H [auth M],
I [auth M],
P [auth L]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
3PH
Query on 3PH

Download Ideal Coordinates CCD File 
C [auth M]
D [auth M]
E [auth M]
G [auth M]
K [auth M]
C [auth M],
D [auth M],
E [auth M],
G [auth M],
K [auth M],
L [auth M],
N [auth L],
Q [auth L]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.2
RECONSTRUCTIONRELION3.1.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00028/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references, Structure summary