Extended Data Figure 6: Representative map quality and model fit and structural analysis of GABA alone, diazepam and flumazenil complexes.

Semitransparent surface is shown for central ligand and contacting side chains for panels a-d. Panel a shows GABA site at chain A-B β-α interface in GABA alone structure. The two β-α GABA sites from the structure superimpose nearly perfectly and do not shed light on the differences in functional contributions found in electrophysiology studies with concatamers⁴⁸. Structures of apo receptor may be essential in identifying structural differences in the two GABA sites. Panel b shows flumazenil site at α-γ interface; panel c shows diazepam at same ECD interface in its structure. Panel d shows bicuculline site at same interface as panel a. Panel e shows picrotoxin site in TMD; here, density is shown for ligand and all nearby protein structure elements. Panel f shows superposition of two GABA plus flumazenil complexes, one from the detergent condition²¹ and one from this study in brain lipids, to illustrate absence of differences in backbone conformation. Note, loops that interact with the TMD do vary in conformation. Panel g shows detail of flumazenil site from the superposition in panel f. Panels h and i show superpositions of three structures from the current study: GABA alone, GABA plus diazepam and GABA plus flumazenil, focused on the two GABA binding sites. Panel j shows calculated interface areas and interaction energies for each subunit pair, for each of the benzodiazepine-related structures.