Fig. 3: VcINDY flexibility changes near the Na1 and Na2 sites between the C_i-Na⁺ state and C_i-apo states.

a Cryo-EM density map in 300 mM NaCl. b. Cryo-EM density map in 100 mM Choline Chloride. In a and b, the respective protein models’ backbones are fitted into the densities. Maps are contoured such that the scaffold domains have equal volume. c. Structure of VcINDY in its C_i-Na⁺ state. d. Structure of VcINDY in its C_i-apo state. In c and d, the structures are colored by normalized B-factors. e NMR-style analysis of the VcINDY structure in Na⁺. f NMR-style analysis of the VcINDY structure in Choline⁺. The resolution for refinement of both structures in e and f was truncated to 3.23 Å. In the absence of sodium, the helices on the cytosolic side of Na1 and Na2, particularly HP_inb and TM10b and their connecting loops, show markedly increase flexibility. Instead of a single structure, the C_i-apo model consists of an ensemble of structures.