The open gate of the AMPA receptor forms a Ca²⁺ binding site critical in regulating ion transport

Alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionic acid receptors (AMPARs) are cation-selective ion channels that mediate most fast excitatory neurotransmission in the brain. Although their gating mechanism has been studied extensively, understanding how cations traverse the pore has remained elusive. Here we investigated putative ion and water densities in the open pore of Ca²⁺-permeable AMPARs (rat GRIA2 flip-Q isoform) at 2.3-2.6 Å resolution. We show that the ion permeation pathway attains an extracellular Ca²⁺ binding site (site-G) when the channel gate moves into the open configuration. Site-G is highly selective for Ca²⁺ over Na⁺, favoring the movement of Ca²⁺ into the selectivity filter of the pore. Seizure-related N619K mutation, adjacent to site-G, promotes channel opening but attenuates Ca²⁺ binding and thus diminishes Ca²⁺ permeability. Our work identifies the importance of site-G, which coordinates with the Q/R site of the selectivity filter to ensure the preferential transport of Ca²⁺ through the channel pore.