Gephyrin and collybistin are key components of
GABA(A) receptor (
GABA(A)R) clustering. Nonetheless, resolving the molecular interactions between the plethora of
GABA(A)R subunits and these clustering
proteins is a significant challenge. We report a direct interaction of
GABA(A)R α2 and α3 subunit intracellular M3-M4 domain (but not α1, α4, α5, α6, β1-3, or γ1-3) with
gephyrin. Curiously,
GABA(A)R α2, but not α3, binds to both
gephyrin and collybistin using overlapping sites. The reciprocal binding sites on
gephyrin for collybistin and
GABA(A)R α2 also overlap at the start of the
gephyrin E domain. This suggests that although
GABA(A)R α3 interacts with
gephyrin,
GABA(A)R α2, collybistin, and
gephyrin form a trimeric complex. In support of this proposal, tri-hybrid interactions between
GABA(A)R α2 and collybistin or
GABA(A)R α2 and
gephyrin are strengthened in the presence of
gephyrin or collybistin, respectively. Collybistin and
gephyrin also compete for binding to
GABA(A)R α2 in co-immunoprecipitation experiments and co-localize in transfected cells in both intracellular and submembrane aggregates. Interestingly,
GABA(A)R α2 is capable of "activating " collybistin
isoforms harboring the regulatory SH3 domain, enabling targeting of
gephyrin to the submembrane aggregates. The
GABA(A)R α2-collybistin interaction was disrupted by a pathogenic mutation in the collybistin SH3 domain (p.G55A) that causes X-linked
intellectual disability and
seizures by disrupting
GABA(A)R and
gephyrin clustering. Because immunohistochemistry in retina revealed a preferential co-localization of collybistin with α2 subunit containing
GABA(A)Rs, but not GlyRs or other
GABA(A)R subtypes, we propose that the collybistin-
gephyrin complex has an intimate role in the clustering of
GABA(A)Rs containing the α2 subunit.