N-methyl-D-aspartate (NMDA) receptors are glutamate-gated calcium-permeable ion channels that are widely implicated in synaptic transmission and plasticity in the brains of vertebrates. The NMDA receptors have a rich pharmacology owing to their ability to bind endogenous and exogenous molecules acting as drug candidates for the treatment of various neurological and psychiatric disorders. Here we report a gallery of cryo-EM structures of the human GluN1-GluN2A NMDA receptor at an overall 4 Å resolution in complex with distinct ligands or modulators. We demonstrate how the ligand binding domains (LBDs) sense the binding of competitive antagonists (CPP and CGP-78608) or agonists (glycine and glutamate) to transduce the signals by closing or opening the ion channel gate within the transmembrane domain (TMD). We also determine that the positive allosteric modulator GNE-6901 binds to the LBD heterodimer interface and subsequently promote the closure of individual LBDs, which further allosterically stretches the opening of the gate. In addition, we unexpectedly visualize the binding pocket of the “foot-in-the-door” blocker 9-aminoacridine (9-AA) at a shallow site above the gate within the LBD-TMD linker region, completely differing from the site of conventional “trapping” blockers within the vestibule of the ion channel. The binding of 9-AA allosterically affects the conformation of the receptor through global compaction. Our study provides molecular insights into the crosstalk between LBDs and TMD during the gating and allosteric transitions. It also unveils an unsuspected site for NMDA receptor channel modulation with potential therapeutic utility.
 

NMDA receptor,Gating mechanism