Structural basis for the subtype-selective activation of K_Ca3.1 channels

The intermediate-conductance (K_Ca3.1) and the small-conductance (K_Ca2.2) Ca²⁺-activated K⁺ channels share a Ca²⁺-calmodulin dependent gating mechanism. We report cryo-electron microscopy structures of K_Ca3.1 and K_Ca2.2 in complex with two benzothiazole-type activators. While SKA-31 is only moderately selective (∼7.3-fold), its derivative SKA-111 exhibits ∼70-fold selectivity for K_Ca3.1 over K_Ca2.2. SKA-31 and SKA-111 both bind in a pocket at the interface between the S₄₅A helix and calmodulin where they allosterically modulate the inner gate of the two channels. SKA-31 binds with comparable energies in the two channels, consistent with its moderate selectivity for K_Ca3.1 over K_Ca2.2. In the K_Ca3.1 structure, the calmodulin helix IV is positioned outward, forming a pocket that more readily accommodates the bulkier SKA-111 that sits deeper inside calmodulin’s N-lobe in K_Ca3.1 than in K_Ca2.2. The resulting higher binding energy explains the improved selectivity of SKA-111 for K_Ca3.1 compared to the less selective SKA-31.