A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly
Figure 2
Illustration of the 2-step ring structure modelling approach for the PrgH periplasmic domain.
(A) In the first step, fixed-backbone symmetric docking was performed starting from the structure of the monomer. The resulting two clusters of ring arrangements cl1 and cl2 differ in the orientation of the C-terminal domain (B). More sampling was then performed, focusing in the vicinity of the two candidate structures, using perturbation symmetric docking runs (see methods) (C). At this step, the backbone is allowed to move to allow for more efficient energy discrimination. While Cluster 2 quickly diverges from the starting-point seed structure (C-cl2), Cluster 1 runs sink into a lower-energy funnel (C-cl1) (starting structures for the perturbation runs are indicated with vertical dashed lines). The final, low-energy ensemble (indicated below the horizontal dashed line in (B-cl1)) shows highly converged features in terms of the backbone conformation and side-chain packing along the interface (D). Only two adjacent subunits of the 24mer complex are shown for simplicity. The RMSDs are computed for backbone atoms of the entire modelled 24mer complex in (A), while in (C) RMSD values are reported for a single dimeric interface relative to the lowest-energy sampled model. The EM map EMD-1875 is used to restrain both steps of docking calculations, although in the last flexible-backbone stage the weights are reduced to one-half relative to the first, rigid-backbone step.