Fig. 1: Overall structure and organization of Thermus thermophilus complex I.

The electron transfer pathway in the peripheral arm (PA) and putative proton translocation pathways in the membrane domain (MD) are indicated by arrows. Complex I subunits are coloured individually and labelled. Fe–S clusters are represented as spheres, with cluster N2 labelled. The quinone is shown as cyan sticks within the quinone-binding cavity (brown surface). The position of its headgroup is based on our DQ data, but the entire ubiquinone tail was modelled to illustrate the extent of the native molecule. In the proton translocation channels, polar residues lining the channels are shown as sticks with carbon in dark blue for the first (N-terminal) half-channel, in green for the second (C-terminal) half-channel, and in orange for the connecting residues. Key residues for antiporter-like subunits, GluTM5 and LysTM7 from the first half-channel, Lys/HisTM8 from the connection, and Lys/GluTM12 from the second half-channel, are labelled. Residues playing similar roles in the E-channel are also labelled (Glu/Asp quartet in red). The central hydrophilic axis extends from the Q site to the tip of the MD along these indicated key residues. The residues connecting quinone cavity to the E-channel are in magenta. Proton translocation pathways through symmetry-related half-channels are indicated by blue arrows, and additional possible paths (extra entry sites and inter-subunit transfer) by violet arrows.