Defining the structural relationship between kainate receptor deactivation and desensitization

Desensitization is an important mechanism that curtails the activity of ligand-gated ion-channels (LGICs). Although the structural basis of desensitization is not fully resolved, it is thought to be governed by the physicochemical properties of the bound ligand. Here, we show the importance of an allosteric cation binding pocket in controlling transitions between activated and desensitized states of rat kainate-type (KAR) ionotropic glutamate receptors (iGluRs). Tethering a positive charge to this pocket sustains KAR activation, preventing desensitization, whereas mutations that disrupt cation binding eliminate channel gating. These different outcomes explain the structural distinction between deactivation and desensitization. Deactivation occurs when the ligand unbinds before the cation, whereas desensitization proceeds if a ligand is bound without cation pocket occupancy. This sequence of events is absent from AMPA-type iGluRs, identifying cations as gatekeepers of KAR gating, a role unique among even closely-related LGICs.