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Structure paper

TitleStructure of the turnover-ready state of an ancestral respiratory complex I.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 9340, Year 2024
Publish dateOct 29, 2024
AuthorsBozhidar S Ivanov / Hannah R Bridges / Owen D Jarman / Judy Hirst /
PubMed AbstractRespiratory 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 ...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.
External linksNat Commun / PubMed:39472559 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 4.5 Å
Structure data

18324

8qby

EMDB-18324, PDB-8qby:
Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs
Method: EM (single particle) / Resolution: 2.3 Å

18325

8qc1

EMDB-18325, PDB-8qc1:
Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement)
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-19975: Respiratory complex I from Paracoccus denitrificans in DDM
Method: EM (single particle) / Resolution: 4.5 Å

EMDB-19976: Respiratory complex I from Paracoccus denitrificans in DDM
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-19977: Cytochrome bc1 complex
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-NA:
Unknown entry

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

ChemComp-CA:
Unknown entry

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

ChemComp-ZN:
Unknown entry

ChemComp-U10:
UBIQUINONE-10

ChemComp-HOH:
WATER

Source
  • paracoccus denitrificans pd1222 (bacteria)
KeywordsOXIDOREDUCTASE / Respiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs

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