Cryo-EM structure of GABA transporter 1 reveals substrate recognition and transport mechanism

The GABA transporters (GATs) enforce spatiotemporal control of the inhibitory neurotransmitter GABA at neural synapses. Nayak et al. report the structure of substrate-bound GAT1 in an ion-bound cytosol-facing conformation, providing mechanistic insights into GABA selection and reuptake. The inhibitory neurotransmitter & gamma;-aminobutyric acid (GABA) is cleared from the synaptic cleft by the sodium- and chloride-coupled GABA transporter GAT1. Inhibition of GAT1 prolongs the GABAergic signaling at the synapse and is a strategy to treat certain forms of epilepsy. In this study, we present the cryo-electron microscopy structure of Rattus norvegicus GABA transporter 1 (rGAT1) at a resolution of 3.1 & ANGS;. The structure elucidation was facilitated by epitope transfer of a fragment-antigen binding (Fab) interaction site from the Drosophila dopamine transporter (dDAT) to rGAT1. The structure reveals rGAT1 in a cytosol-facing conformation, with a linear density in the primary binding site that accommodates a molecule of GABA, a displaced ion density proximal to Na site 1 and a bound chloride ion. A unique insertion in TM10 aids the formation of a compact, closed extracellular gate. Besides yielding mechanistic insights into ion and substrate recognition, our study will enable the rational design of specific antiepileptics.