(a) The crystal structure of the NavMs pore depicted in ribbon representation13. The regions in one of the four monomers are coloured according to the scheme in Fig. 1 (blue for the S6 helix, magenta for the S5 helix, green for P1, yellow for P2 and red for the SF), with the other three monomers depicted in grey for clarity. (b) Electrostatic representation of the NavMs pore (from the membrane normal direction), showing that the entire surface is very hydrophobic. (c) Overlaid structures of the NavMs (red) and NavAb (blue) pores depicted in ribbon representations, showing that they are very similar in all regions except the C-terminal end of S6 (closest to the intracellular surface), where they deviate significantly. The directions of the motions are indicated by the yellow arrows. A video morphing between the open and closed structures is included as Supplementary Movie 1. (d) Comparison of the electrostatic surfaces14 of the NavMs symmetric pore model (based on a tetramer constructed from the most bent monomer) and the NavAb pore, viewed along the membrane normal and sliced through the middle of the tetramer (top) and from the cytoplasmic surface (bottom). (e) Plot of residue number versus RMSD (root mean square deviation) differences between NavMs (chain A) and NavAb (chain A) Cα positions in the S6 helix, showing that the major differences occur starting at residue Thr209 (indicated by the yellow box). The colours of the names of the residues identified on the model are reflected in the colour of the points on the plot. (f) Stereo electron density map (2Fo–Fc, 1 σ-contour) of the open-channel conformation (red) backbone atoms overlaid on the closed-channel conformation backbone atoms (blue), which clearly shows the deviation of the structures at the bottom of the S6 helix.