Figure 6.

Illustration of the evaluation process of the ring-models. The predicted models (Fig. 5) are further discriminated by experimentally derived data of accessible and buried lysine residues, identified by limited biotinylation (Supplementary Fig. 3). The models in panels a – f show a representative subset of models to illustrate the process in detail. Solvent accessible residues are rendered in green and buried in yellow spheres. In addition we utilized site-directed mutagenesis data on two negatively charged patches of EscC that show defects in type III secretion upon mutation (residues in orange spheres) (Supplementary Fig. 4). The illustrated process identifies a subset of models that all satisfy both the modeling/structural constraints and the experimental data (the models a, b, c, d and e are representative for the identified subset; the model f can be excluded because it does not meet the experimental data). This ensemble of validated models was further evaluated by docking to the EM density maps of the T3SS basal body and NC from S. typhimurium ⁵, ²¹. This process led to a set of final models that fulfil all structural/modelling, experimental and docking constrains. In the representative subset above only models a and b show considerable complementarity to the periplasmic regions of the EM density maps and satisfy all imposed criteria (Supplementary Fig. 8). These two models and their docking positions are equivalent to the models described in Figure 3b.