Considerable evidence indicates the second transmembrane domain (TM2) of the ␥-aminobutyric acid (GABA) receptor lines the integral ion pore. To further delineate the structures that constitute the ion pore and selectivity filter of the 1 GABA receptor, we used the substituted cysteine accessibility method with charged reagents to identify anion-and cation-accessible surfaces. Twenty-one consecutive residues were mutated to cysteine, one at a time, in the presumed intracellular end of the first transmembrane domain (TM1; Ala 271 -Met 276 ), the entire linker connecting TM1 to TM2 (Leu 277 -Arg 287 ), and the presumed intracellular end of TM2 (Ala 288 -Ala 291 ). Positively (MTSEA ؉ ) and negatively (pCMBS ؊ ) charged sulfhydryl reagents, as well as Cd 2؉ , were added extracellularly to test accessibility of the engineered cysteines. Four of the mutants, all at the intracellular end of TM2 (R287C, V289C, P290C, A291C), were accessible to positively charged reagents, whereas seven mutants (A271C, T272C, L277C, W279C, V280C, P290C, A291C) were functionally modified by negatively charged pCMBS ؊ . These seven modified residues were at the intracellular end of TM2, in the TM1-TM2 linker, and at the intracellular end of TM1. In nearly all cases (excluding P290C), the rate and the degree of modification were state-dependent, with greater accessibility in the presence of agonist. Select cysteine mutants were combined with a point mutation (A291E) that converted the pore from chloride-to non-selective. In this case, positively charged reagents could modify residues in the TM1-TM2 linker (Leu 277 and Val 280 ), supporting the notion that the modifying reagents were reaching their target through the pore. Taken together, our results suggest that, up to its intracellular end, the TM2 domain is not charge selective. In addition, we propose that the TM1-TM2 linker and the intracellular end of TM1 are along the pathway of the permeating ion. These findings may lend new insights into the structure of the GABA receptor pore.Ligand-gated ion channels play a fundamental role in neuronal communication. The ␥-aminobutyric acid (GABA) 1 receptor is the major inhibitory neurotransmitter-activated ion channel in mammalian brain and is an important target for a variety of clinically prescribed therapeutic compounds. Detailed knowledge of its structure and function can provide important information for understanding the fundamentals of neuronal communication, the treatment of neurological disorders, and the design of therapeutic compounds that target the GABA receptor.The family of ligand-activated ion channels that includes the GABA, nicotinic acetylcholine (nACh), glycine, and serotonin type 3 receptors (1-5) is composed of a group of proteins with diverse functional properties but homologous structure. This structure includes four predicted transmembrane domains (TM1-TM4), a large extracellular amino-terminal domain containing the agonist-binding site, and a large intracellular linker between TM3 and TM4 that has been suggested to pla...