Crystal structure at 1.95 angstrom resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition

The anti-breast tumour antibody SM3 has a high selectivity in reacting spec ifically with carcinoma-associated mucin. SM3 recognises the core repeating motif (Pro-Asp-ThP-Arg-Pro) of aberrantly glycosylated epithelial mucin MU C1, and has potential as a therapeutic and diagnostic tool. Here we report the crystal structure of the Fab fragment of SM3 in complex with a 13-resid ue MUC1 peptide antigen (Thr1P-Ser2P-Ala3-Pro4P-Asp5P-Thr6P-Arg7P-Pro8P-Ala 9P-Pro10P- Gly11P-Ser12P-Thr13P). The SM3-MUC1 peptide structure was solved by molecular replacement, and the current model is refined at 1.95 Angstro m resolution with an X-factor of 21.3% and R-free 28.3%. The MUC1 peptide i s bound both by non-polar interactions and hydrogen bonds in an elongated g roove in the antibody-combining site through interactions with Complimentar ity Determining Regions (CDRs), three of the light chain (L1, L2, L3) and t wo of the heavy chain (H1 and H3). The conformation of the peptide is mainl y extended with no discernable standard secondary structure. There is a sin gle non-proline cis-peptide bond in H3 (Va195H-Gly96H-Gln97H-Phe98H-Ala101H -Tyr102H) between Gly96H and Gln97H, which appears to play a role in SM3-pe ptide antigen interactions, and represents the first such example within an antibody hypervariable loop. The SM3-MUC1 peptide structure has implicatio ns for rational therapeutic and diagnostic antibody engineering. (C) 1998 A cademic Press.