The architecturally complex secretory granules of Paramecium, known as trichocysts, have two unusual and seemingly contradictory features: their protein contents have crystalline organization (Sperling, L., Tardieu, A., and Gulik-Krzywicki, T. (1987) J. Cell Biol. 105, 1649-1662), yet these proteins are a heterogeneous set of molecules encoded by a large multigene family (Madeddu, L., Gautier, M.-C., Vayssié, L., Houari, A., and Sperling, L. (1995) Mol. Biol. Cell 6, 649-659). We present here the first complete sequences of three genes coding for three different precursors of the trichocyst crystalline matrix proteins. The deduced protein sequences indicate that each precursor gives rise to two of the mature polypeptides found in the crystalline trichocyst matrix. Analysis of putative processing sites suggests that a series of reactions, some of which may involve a novel endopeptidase, are involved in their proteolytic maturation. Each of the 6 mature polypeptides contains heptad segments. Characterization of the heptad segments leads us to propose that the mature polypeptides that compose the crystalline trichocyst matrix, despite their different primary structures, all share a unique protein fold, probably a 4 alpha-helical antiparallel bundle.