Fig. 3: Proton pathway in both hemi channels with water densities.

A The surface properties of the transmembrane region of a-subunit. The surface of the a-subunit is colored cyan (hydrophilic) to yellow (hydrophobic). B The coordination of water molecules in the half-channels. The cryo-EM water molecules are shown in sphere representation and colored by density from the MD simulation. The color scale illustrates the relative density of water, with the bulk density set to 1. The iso-surface of the relative water density of 0.5 obtained from MD simulation is shown with the cryo-EM water molecules. The regions indicated by the dashed rectangles are enlarged in (C, D). Enlarged views of the periplasmic (C) and cytoplasmic (D) channels. The residues forming the channels are shown in stick representation. The dashed line in (C) indicates the possible proton relay path. E The possible proton relay path. The cryo-EM water molecules are represented as spheres with the same color coding as (B–D).