Extended Data Fig. 8: Architecture of the ubiquinol/ubiquinone (Q) binding sites in Arabidopsis complex III2.
a, The Qo site. One proton from bound ubiquinol can be transferred directly to H237 of the Rieske head domain in the b-state (black dotted line). The second proton can be released into the bulk solvent of the lumen (red arrows) along a chain of water molecules towards Cyt b H259 or towards a pool of water molecules (dotted blue ellipse) involving Cyt b Y280 and the heme bL propionate group. The sidechain of Cyt b E278 of the Qo motif faces away from the ubiquinol (black arrow) and its carboxylate group is not in hydrogen bond distance to the substrate or the water chain (grey dotted lines). b, The Qi site. Proton transfer from the bulk solvent of the matrix (blue arrows) towards a carbonyl group of bound ubiquinon can proceed via two hydrogen bond networks from clusters of water molecules (blue ellipses). One of them is surrounded by subunit QCR7, the N-terminal part of the Rieske protein, subunit Cyt c1, Cyt b and three bound lipids (two cardiolipins, CL; one phosphatidylcholine, PC). From this pool, protons can be accepted by Cyt b K234 from where they can pass to the bound ubiquinone across Cyt b D235. The other proton transfer pathway involves Cyt b K224. Our structure indicates that Cyt b H208 participates in proton transfer by forming a direct hydrogen bond to ubiquinone. Red dots, water molecules; black dotted lines, hydrogen bonds. Colors of the protein subunits (Cyt c1, Cyt b, Rieske, QCR7) as in Fig. 2. Q is drawn in pink.
