The 5-HT3 (5-hydroxytryptamine) receptor is a typical member of the Cys-loop family of ligand-gated ion channels. No atomic resolution structures of these proteins have yet been published, and thus structure–function relationships in this family of proteins have been largely determined from experimental evidence combined with the use of homologous proteins and lower resolution images. Here, recent advances in our knowledge of the structure and function of the transmembranous part of the 5-HT3 receptor are reviewed. These show that the pore region, M2, is largely α-helical, and ion selectivity may be controlled by charged amino acid rings at each end of this pore region. The mechanism by which the pore opens is probably similar to that proposed for the nACh receptor, i.e. a twist of M2, caused by rotation in the extracellular domains, removes hydrophobic residues from the ion path.

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