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Significance Determination of the structure of ion channels in their physiologically relevant states remains a major challenge. Structural models of the unliganded closed-channel and the fully liganded open-channel conformations of different members of the nicotinic-receptor superfamily have been generated using cryoelectron microscopy or X-ray crystallography. In this paper, we describe the structure of what appears to be the closed-channel conformation in its liganded state. We used X-ray crystallography to solve the structure of two mutants of a proton-gated bacterial ortholog that exhibit a reduced equilibrium constant for the closed-to-open transition; to favor the ligand-bound state, the crystals were grown at pH ∼4.0. Compared with the liganded open-channel conformation, the closed-channel conformation presents a narrower pore, but an indistinguishable extracellular domain.

Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography