Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain

Zinc is vastly present in the mammalian brain and controls functions of various cell surface receptors to regulate neurotransmission. A distinctive characteristic of N-methyl-D-aspartate (NMDA) receptors containing a GluN2A subunit is that their ion channel activity is allosterically inhibited by a nano-molar concentration of zinc that binds to an extracellular domain called an amino-terminal domain (ATD). Despite physiological importance, the molecular mechanism underlying the high-affinity zinc inhibition has been incomplete because of the lack of a GluN2A ATD structure. Here we show the first crystal structures of the heterodimeric GluN1-GluN2A ATD, which provide the complete map of the high-affinity zinc-binding site and reveal distinctive features from the ATD of the GluN1-GluN2B subtype. Perturbation of hydrogen bond networks at the hinge of the GluN2A bi-lobe structure affects both zinc inhibition and open probability, supporting the general model in which the bi-lobe motion in ATD regulates the channel activity in NMDA receptors. •Structure of the GluN1-GluN2A ATD heterodimer is obtained for the first time•The high-affinity zinc-binding site in GluN2A is completely mapped•Elements for subtype-specific binding of zinc and phenylethanolamine are found•Inter-lobe interface of ATD controls zinc inhibition and channel open probability NMDA receptors are regulated by allosteric modulators. Romero-Hernandez et al. show the first crystal structure of the GluN1-GluN2A amino-terminal domain, which illuminates the molecular determinants for subtype-specific allosteric inhibition by zinc and ifenprodil in NMDA receptors.