The 5-HT3 receptor is a cation-selective ligand-gated ion channel of the Cys-loop superfamily. The receptor is an important therapeutic target, with receptor antagonists being widely used as antiemetics in cancer therapy. The two known receptor subunits, A and B, form homomeric 5-HT 3A receptors and heteromeric 5-HT3A/B receptors. The heteromeric receptor has the higher single-channel conductance and more closely mimics the properties of the native receptor. We have used atomic force microscopy to study the architecture of 5-HT 3A and 5-HT3A/B receptors. We engineered different epitope tags onto the A-and B-subunits and imaged receptors that were doubly liganded by anti-epitope antibodies. We found that, for the 5-HT 3A/B receptor, the distribution of angles between antibodies against the A-subunit had a single peak at Ϸ144°, whereas the distribution for antibodies against the B-subunit had two peaks at Ϸ72°and 144°. Our results indicate that the subunit stoichiometry is 2A:3B and that the subunit arrangement around the receptor rosette is B-B-A-B-A. This arrangement may account for the difference between the agonist Hill coefficients and the single-channel conductances for the two types of receptor.ligand-gated ion channel ͉ receptor structure T he 5-HT 3 receptor is a member of the Cys-loop ligand-gated ion channel superfamily, together with the nicotinic acetylcholine receptor, the GABA A receptor, and the glycine receptor (1-3). Electron microscopy of the affinity purified 5-HT 3 receptor has shown that it contains five subunits arranged pseudosymmetrically around a cylinder of long axis 11 nm and external diameter 8 nm (4, 5). The vestibule of the channel, normally open to the cell exterior, is visible as an opening of diameter 2-3 nm. Two 5-HT 3 receptor subunits have been investigated in detail. The first to be cloned, 5-HT 3A (6), expresses as a functional homomer, whereas the second, 5-HT 3B , is unable to form functional channels alone but expresses robustly in the presence of the 5-HT 3A subunit (7). The genes for these two subunits are located in close proximity on chromosome 11, although additional putative 5-HT 3 receptor genes have been isolated on chromosome 3 (8). The biophysical properties of the 5-HT 3A and the 5-HT 3A/B receptors exhibit significant differences, with those of the heteromer more closely resembling those of the receptor characterized within the majority of mammalian systems (9-12). Competitive antagonists of 5-HT 3 receptors are used clinically as antiemetics in cancer chemotherapy and in general anesthesia, although other applications are being explored (13). The two receptor subtypes are difficult to distinguish pharmacologically (14), although picrotoxin (15) and tubocurarine (7) are markedly less potent in blocking agonist-induced currents in the exogenously expressed heteromeric receptors. Although there is some anatomical evidence that the homomeric receptor may be expressed alone in the rat (16, 17), current functional evidence suggests that it is the heteromer that is o...