A large cytoplasmic domain accounts for approximately onethird of the entire protein of one superfamily of ligand-gated membrane ion channels, which includes nicotinic acetylcholine (nACh), ␥-aminobutyric acid type A (GABA A ), serotonin type 3 (5-HT 3 ), and glycine receptors. Desensitization is one functional feature shared by these receptors. Because most molecular studies of receptor desensitization have focused on the agonist binding and channel pore domains, relatively little is known about the role of the large cytoplasmic domain (LCD) in this process. To address this issue, we sequentially deleted segments of the LCD of the 5-HT 3A receptor and examined the function of the mutant receptors. Deletion of a small segment that contains three amino acid residues (425-427) significantly slowed the desensitization kinetics of the 5-HT 3A receptor. Both deletion and point mutation of arginine 427 altered desensitization kinetics in a manner similar to that of the (425-427) deletion without significantly changing the apparent agonist affinity. The extent of receptor desensitization was positively correlated with the polarity of the amino acid residue at 427: the desensitization accelerates with increasing polarity. Whereas the R427L mutation produced the slowest desensitization, it did not significantly alter single channel conductance of 5-HT 3A receptor. Thus, the arginine 427 residue in the LCD contributes to 5-HT 3A receptor desensitization, possibly through forming an electrostatic interaction with its neighboring residues. Because the polarity of the amino acid residue at 427 is highly conserved, such a desensitization mechanism may occur in other members of the Cys-loop family of ligand-gated ion channels.The Cys-loop pentameric ligand-gated ion channel (LGIC) 2 superfamily includes nicotinic acetylcholine (nACh), ␥-aminobutyric acid type A (GABA A ), glycine, and serotonin type 3 (5-HT 3 ) receptors (1). These receptors play crucial roles in fast synaptic transmission through agonist-induced opening of transmembrane ion channels in the central and peripheral nervous systems. Topologically, these receptors consist of a large extracellular N-terminal domain, a large cytoplasmic domain (LCD), and four transmembrane domains (1). The 5-HT 3 receptor can modulate the release of neurotransmitters such as glutamate, GABA, and dopamine (DA), and plays a role in the reward mechanisms of drug addiction (2, 3). Of all five 5-HT 3 subunits identified by molecular cloning, the 5-HT 3A and 5-HT 3B subunits have been the most thoroughly characterized (4). Although the 5-HT 3B subunit can form a functional heteromer when co-expressed with the 5-HT 3A subunit (5), the 5-HT 3A subunit is capable of forming a functional channel (1), and such a homomer is thought to be the dominant functional form in the central nervous system (6).One common feature shared by members of the LGIC superfamily is that these receptors desensitize at synaptic sites when exposure to agonist is prolonged. Desensitization plays a critical role in the...