Supplementary Figure 2: Crystal structure of VcINDY compared with the repeat-swapped model.

(a) The X-ray crystal structure of a VcINDY protomer in an inward-facing conformation (left) is compared with the repeat-swapped protomer model in an outward-facing conformation (right). Structures are viewed along the plane of the membrane, with the extracellular side at the top. The Bendix plugin [Dahl A.C.E., Chavent M., Sansom M.S.P., Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics 2012;28:2193–4] to the program VMD [Humphrey, W., Dalke, A. and Schulten, K., VMD - Visual Molecular Dynamics, J Molec Graphics 1996;14:33-38] was used to represent the helices. To quantify the conformational change of the protein, the rotation axis, rotation angle, and displacement of the helices were evaluated. The black line indicates the rotation axis, which lies approximately perpendicular to the symmetry axis. The displacement values suggest an elevator-like movement of the transport domain containing the substrates (spheres) across the membrane, and this displacement is associated with a rotation of 43°. (b) Displacement per residue was determined as the distance between Cα atoms in the crystal structure and the model (black line) after aligning the structures using the scaffold domain. Note that the model built prior to adding intradomain restraints, while using the same refined alignment (“Refined model”, red line) implies a similar conformational change in the transport domain relative to the scaffold as the model built using intradomain restraints (“Final model”, black line). By this analysis, the transport domain can be considered to comprise helices HP1-TM5-TM6 and HP2-TM10-TM11.