The second messenger, inositol 1,4,5-trisphosphate (InsP3) transduces many hormonal signals which regulate Ca(2+)-dependent processes in the intestinal epithelium. To study the receptors for InsP3 (InsP3Rs), which function as intracellular Ca2+ channels, cDNA clones encoding InsP3Rs were isolated from a human colon adenocarcinoma cell line, HT29. The majority of clones encoded the type 3 InsP3R, the product of the ITPR3 gene on chromosome 6, for which only a 147-amino-acid fragment was known previously (Ozcelik, T., Sudhof, T. C., and Francke, U. (1991) Cytogenet. Cell Genet. Abstr. 58, 1880; Sudhof, T. C., Newton, C. L., Archer, B. T., III, Ushkaryov, Y. A., and Mignery, G. A. (1991) EMBO J. 10, 3199-3206). The complete sequence of the type 3 InsP3R polypeptide (2,671 amino acids) is described here. Primary structure analysis indicates a pattern of conserved and variable regions which is characteristic of the InsP3R family. A 250-kDa protein (SDS-PAGE) which specifically binds InsP3 is immunoprecipitated by affinity-purified antibodies raised against a COOH-terminal fusion protein. Transient expression in COS-7 cells of a polypeptide comprising the NH2-terminal 750 amino acids establishes that the ligand-binding domain is localized to this region. Lysates from transfected COS-7 cells bind InsP3 with high affinity (Kd = 151 nM) compared with other inositol phosphates (InsP3 > Ins 1,3,4,5-P4 > InsP6 > Ins 1,4-P2 > Ins 1-P). Immunocytochemical localization in the intestine reveals expression in crypt and villus epithelial cells, but not in cells of the lamina propria, submucosa, or muscularis layers. The subcellular distribution and appearance of staining is consistent with localization on the endoplasmic reticulum, with the highest concentration of staining occurring adjacent to the apical brush border of villus cells.