Amoebapore, the pore-forming peptide of E histolytica has been isolated and its structure elucidated on the cDNA and protein level. The peptide is composed of 77 amino acid residues including six cysteine residues and has a molecular mass of 8244 Da. The primary translation product contains a signal sequence of 21 mostly hydrophobic amino acid residues. The active peptide has been located in the cytoplasmic granules of the amoebae. Circular dichroism spectroscopy revealed an all alpha-helical conformation and computer-aided secondary structure prediction yielded a structure of four helices. The helical conformation and three intramolecular disulfide bonds impart a highly compact and rigid structure upon the molecule. The activity of amoebapore, measured by a liposome depolarization assay, is resistant to heating at 100-degrees-C in the absence of reducing agents. Synthetic peptides corresponding to the helices 1 and 3 exhibited pore-forming activity. Two minor, biologically active isoforms of amoebapore have amino acid sequence identity of 57% and 47%, respectively. Whereas amoebapore is a constituent of pathogenic E histolytica isolates, nonpathogenic E histolytica produce a structurally very similar peptide, the specific activity of which is approximately one third that of amoebapore. The biological significance of amoebapore for the pathogenicity of E histolytica and specifically for its cytolytic activity remains to be determined.