Bioenergetics

Protein subunit

ATP synthase

Enzyme

Yarrowia

Biology

Gene

Biophysics

Chemistry

Yeast

Mitochondrion

Biochemistry

Nature Structural & Molecular Biology

Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-Å-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian ‘deactive transition’ (relevant to ischemia–reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine. A cryo-EM structure of mitochondrial complex I from Yarrowia lipolytica reveals structured waters involved in proton relays and energy transfer, with insights into the ‘deactive transition’ in mammalian systems.

Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation