6Y79

Cryo-EM structure of a respiratory complex I F89A mutant

Summary for 6Y79

• Entry DOI: 10.2210/pdb6y79/pdb
• EMDB information: 10711
• Descriptor: Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I), Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I), Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I), ... (55 entities in total)
• Functional Keywords: complex i, nadh dehydrogenase, mitochondrion proton pumping, ubiquinone, oxidoreductase
• Biological source: Yarrowia lipolytica (Candida lipolytica); More
• Total number of polymer chains: 42
• Total formula weight: 1010742.05

Authors

Parey, K. (deposition date: 2020-02-28, release date: 2020-10-28, Last modification date: 2024-10-16)

Primary citation

Galemou Yoga, E.,Parey, K.,Djurabekova, A.,Haapanen, O.,Siegmund, K.,Zwicker, K.,Sharma, V.,Zickermann, V.,Angerer, H.
Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I.
Nat Commun, 11:6008-6008, 2020

PubMed Abstract: Respiratory complex I catalyzes electron transfer from NADH to ubiquinone (Q) coupled to vectorial proton translocation across the inner mitochondrial membrane. Despite recent progress in structure determination of this very large membrane protein complex, the coupling mechanism is a matter of ongoing debate and the function of accessory subunits surrounding the canonical core subunits is essentially unknown. Concerted rearrangements within a cluster of conserved loops of central subunits NDUFS2 (β1-β2 loop), ND1 (TMH5-6 loop) and ND3 (TMH1-2 loop) were suggested to be critical for its proton pumping mechanism. Here, we show that stabilization of the TMH1-2 loop by accessory subunit LYRM6 (NDUFA6) is pivotal for energy conversion by mitochondrial complex I. We determined the high-resolution structure of inactive mutant F89A of eukaryotic complex I from the yeast Yarrowia lipolytica and found long-range structural changes affecting the entire loop cluster. In atomistic molecular dynamics simulations of the mutant, we observed conformational transitions in the loop cluster that disrupted a putative pathway for delivery of substrate protons required in Q redox chemistry. Our results elucidate in detail the essential role of accessory subunit LYRM6 for the function of eukaryotic complex I and offer clues on its redox-linked proton pumping mechanism.

PubMed: 33243981
DOI: 10.1038/s41467-020-19778-7

Experimental method

ELECTRON MICROSCOPY (2.96 Å)