<p>Kainate receptors (KARs), a distinct subfamily of ionotropic glutamate receptors, are critical modulators of synaptic transmission and network excitability. Their function is intricately regulated by auxiliary subunits and endogenous ions. The GluK3 subunit, in particular, exhibits unique gating and modulatory properties; however, the interplay between its known regulators, the Neto auxiliary proteins, and synaptic zinc remains poorly understood. We reveal a multi-layered regulatory system governing the function of GluK3. Using whole-cell electrophysiology, we demonstrate that the auxiliary subunits Neto1 and Neto2 differentially regulate the gating kinetics of GluK3. While both proteins markedly slow receptor desensitization and relieve the intrinsic polyamine block, they exert opposing effects on the rate of recovery from desensitization, with Neto1 accelerating and Neto2 decelerating recovery, suggesting distinct mechanisms for tuning synaptic fidelity. Crucially, we show that Neto proteins uniquely reshape the potentiation of GluK3 currents by zinc. Neto2, in particular, acts synergistically with zinc to produce a profound facilitation of peak currents. To dissect these regulatory pathways, we utilized a GluK3 (D759G) mutant, which ablates the LBD dimer interface zinc-binding site. This mutation unmasked a secondary, inhibitory zinc-binding site, revealing a previously unknown layer of modulation. While the (D759G) mutant preserved the fundamental modulatory actions of Neto proteins, the Neto isoforms differentially regulated this previously unidentified revealed inhibitory zinc effect. Cryo-electron microscopy confirms that the (D759G) mutation promotes a more compact arrangement of the ligand-binding domain (LBD), consistent with its stabilizing effect on gating. Together, these findings establish a distinct framework for understanding KAR function, where auxiliary subunits and ionic modulators converge to create a highly tunable signaling complex essential for synaptic plasticity.</p>