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Significance Phospholipid membranes often contribute a large fraction of the environment to which integral membrane proteins are exposed. As a result, the behavior of these proteins is commonly affected by solubilization in detergent micelles or even by the particular chemical composition of the lipid bilayer in which they are embedded. In this work, we report cryoelectron microscopy structures of the bacterial pentameric ligand-gated ion channel ELIC embedded in nanodiscs formed by palmitoyl-oleoyl-phosphatidylcholine (POPC) molecules alone, a lipid composition that reduces this channel’s activity to a large extent. Comparison of the unliganded and agonist-bound structural models suggests that POPC membranes disrupt the strict coupling between binding-site affinity and pore permeability that underlies the operation of all ligand-gated ion channels.

Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer