(A) Model built based on the SecYEG–SecA crystal structure (PDB code 3DIN [29]) which has been allowed to relax with MD simulations (full details to be published separately). The proteins are shown as cartoons, with SecA in light blue, SecY in pink, SecE in light orange and SecG in light green, with a bound ATP molecule shown as orange, blue, white and red spheres. A prospective pathway for a model substrate (the first 76 residues of pro-OmpA; shown as dark blue cartoon and mesh) has been built into the channel based on known cross-linking sites in SecA (pink, red, blue and white spheres; [35]) and the position of the SecY pore ring [30]. The helical SS was built based on the density of the DsbA SS from a recent cryo-EM structure of the SecY complex bound to a ribosome (inset–DsbA SS light blue, with the density shown using map EMD-5693, at 3.0 sigma within 2.6 Å of the selection [13]). (B) Close-up of the channel from (A) with the substrate, LG and 2HF shown as dark blue, pink and teal mesh respectively. The pore ring residues of SecY are highlighted in red.