  Glutamate-gated kainate receptors (KARs) are ubiquitous in the central
nervous system of vertebrates, mediate synaptic transmission on post-synapse,
and modulate transmitter release on pre-synapse. In the brain, the trafficking,
gating kinetics, and pharmacology of KARs are tightly regulated by Neuropilin
and tolloid-like proteins (Netos). Here we report cryo-EM structures of
homo-tetrameric GluK2 in complex with Neto2 at inhibited and desensitized
states, illustrating variable stoichiometry of GluK2-Neto2 complexes, with one
or two Neto2 subunits associate with the GluK2. We find that Neto2 accesses
only two broad faces of KARs, intermolecularly crosslinking the lower-lobe of
ATDA/C, upper-lobe of LBDB/D, and lower-lobe of LBDA/C, illustrating how Neto2
regulates receptor-gating kinetics. The transmembrane helix of Neto2 is
positioned proximal to the selectivity filter and competes with the amphiphilic
H1-helix after M4 for interacting with an ICD formed by the M1-M2 linkers of
the receptor, revealing how rectification is regulated by Neto2.
