Cryo-EM structure of the human α1β3γ2 GABA(A) receptor in a lipid bilayer

Type A γ-aminobutyric acid receptors (GABA(A)Rs) are pentameric ligand-gated ion channels (pLGICs) and the main drivers of fast inhibitory neurotransmission in the vertebrate nervous system1,2. Their dysfunction is implicated in a range of neurological disorders, including depression, epilepsy and schizophrenia3,4. Amongst the numerous assemblies theoretically possible, α1β2/3γ2 GABA(A)Rs are most prevalent in the brain5. The β3 subunit plays an important role in maintaining inhibitory tone and expression of this subunit alone is sufficient to rescue inhibitory synaptic transmission in a CRISPR/Cas9 derived β1-3 triple knockout6. To date, efforts to generate accurate structural models for heteromeric GABA(A)Rs have been hampered by the use of engineered receptors and the presence of detergents7–9. Significantly, some recent cryo-EM reconstructions report “collapsed” conformations8,9 which disagree with the prototypical pLGIC, the Torpedo nicotinic acetylcholine receptor10,11, the large body of structural work on homologous homopentameric receptor variants12, and the logic of a ion channel architecture. To address this problem, here we present a high-resolution cryo-EM structure of the full-length human α1β3γ2L, a major synaptic GABA(A)R isoform, functionally reconstituted in lipid nanodiscs. The receptor is bound to a positive allosteric modulator megabody and in a desensitised conformation. Unexpectedly, each GABA(A)R pentamer harbours two phosphatidylinositol 4,5-bisphosphate (PIP2) molecules, whose head groups occupy positively-charged pockets in the intracellular juxtamembrane regions of α1-subunits. Beyond this level, the intracellular M3-M4 loops are largely disordered, possibly because interacting post-synaptic proteins were not included. This structure illustrates the molecular principles of heteromeric GABA(A) receptor organization and provides a reference framework for future mechanistic investigations of GABA-ergic signalling and pharmacology.