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TitleCryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 2758, Year 2022
Publish dateMay 19, 2022
AuthorsInjae Chung / John J Wright / Hannah R Bridges / Bozhidar S Ivanov / Olivier Biner / Caroline S Pereira / Guilherme M Arantes / Judy Hirst /
PubMed AbstractMitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q) and drive four protons across the inner mitochondrial membrane, powering ...Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, the mechanisms of Q reduction and energy transduction remain controversial. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q. Using cryo-EM, we reveal a Q molecule occupying the full length of the Q-binding site in the 'active' (ready-to-go) resting state together with a matching substrate-free structure, and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q binding pose. By comparing ligand-bound and ligand-free forms of the 'deactive' resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance.
External linksNat Commun / PubMed:35589726 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 3.02 Å
Structure data

EMDB-14132, PDB-7qsk:
Bovine complex I in lipid nanodisc, Active-Q10
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-14133, PDB-7qsl:
Bovine complex I in lipid nanodisc, Active-apo
Method: EM (single particle) / Resolution: 2.76 Å

EMDB-14134, PDB-7qsm:
Bovine complex I in lipid nanodisc, Deactive-ligand (composite)
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-14139, PDB-7qsn:
Bovine complex I in lipid nanodisc, Deactive-apo
Method: EM (single particle) / Resolution: 2.81 Å

EMDB-14140, PDB-7qso:
Bovine complex I in lipid nanodisc, State 3 (Slack)
Method: EM (single particle) / Resolution: 3.02 Å

Chemicals

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

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

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-U10:
UBIQUINONE-10

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

ChemComp-K:
Unknown entry

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-ZN:
Unknown entry

ChemComp-EHZ:
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate

ChemComp-CHD:
CHOLIC ACID

ChemComp-MYR:
MYRISTIC ACID

ChemComp-HOH:
WATER

ChemComp-GOL:
GLYCEROL

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

Source
  • bos taurus (cattle)
  • cattle (cattle)
KeywordsOXIDOREDUCTASE / Mitochondrial complex I / Respiratory complex I / NADH:ubiquinone oxidoreductase / Ubiquinone / Nanodisc / ELECTRON TRANSPORT

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