Fig. 6. Proton transfer path in the membrane arm of Arabidopsis complex I.

a, Conserved amino acids and water molecules (red spheres) in the membrane arm mark the central aqueous passage (white continuous line) and potential water channels (white dashed lines) to the mitochondrial matrix (transparent blue) or the cristae lumen (transparent red). The passage is interrupted at transmembrane helix 3 of subunit ND6 (red bars; see b). In subunit ND2, two potential half-channels connect the central aqueous passage to the matrix or the lumen. C1-FDX with its bound Fe ion sits next to the entrance of the ND2 matrix half-channel. The matrix and lumenal half-channel of ND5 are open. Proton leakage is prevented by a ~6 Å gap between ND5 H257 and T315 of the aqueous passage (red dotted line). b, π-Gate at the TMH3 of ND6 seen from the matrix side. Core subunits of the membrane arm are represented in shades of blue. The water chain in the central aqueous passage is interrupted by a ~9.1 Å gap. c, Density and fitted atomic model of the map region where C1-FDX (magenta) interacts with ND2 at the entrance to the potential aqueous half-channel that would connect the matrix to the central aqueous passage. The horizontal black line indicates that under our experimental conditions the channel is closed.