Supplementary Figure 7: Comparison of the models generated with and without intradomain restraints with the VcINDY X-ray structure (PDB 4F35).

(a) Cartoon representation of the model obtained before applying distance restraints within the scaffold and transport domains (“refined model”) and the model obtained after applying restraints (“final model”) and the VcINDY structure used as template. Note that the alignment used to build both models is the same. The repeat-swapped models were built and refined as protomers, and then duplicated to construct the dimer model (see Methods). Therefore individual protomers are shown here, though the final model is a dimer. The coloring scheme is that used in the transmembrane definition and the substrate mimic (citrate) and one sodium ion are shown as green, red, and purple spheres. (b) The coloring scheme reflects the conservation level identified using ConSurf [Ashkenazy H, Erez, E., Martz, E., Pupko, T. and Ben-Tal, N., ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 2010;38:W529–W533].