Calcium stabilization of a flexible N-terminal domain in a pentameric ligand-gated ion channel

Pentameric ligand-gated ion channels (pLGICs) are responsible for the rapid conversion of chemical to electrical signals. In addition to the canonical extracellular and transmembrane domains, some prokaryotic pLGICs contain an N-terminal domain (NTD) of unclear structure and function. In one such case, the calcium-sensitive channel DeCLIC, the NTD appears to accelerate gating; however, its evident flexibility has posed a challenge to model building, and its role in calcium sensitivity is unclear. Here we report cryo-EM structures of DeCLIC to the highest resolutions thus far, in circularized lipid nanodiscs. Application of refinement tools enabled definition of multiple calcium-binding sites in each symmetric subunit. Under calcium-free conditions, both symmetric and asymmetric classes could be reconstructed, implicating a heterogeneous ensemble. Behavior of these structures in molecular dynamics simulations was consistent with calcium stabilization of the NTD, an effect that may be conserved in structurally homologous domains across evolution.