An unusual human IgM antibody with a protruding HCDR3 and high avidity forits peptide ligands

The crystal structure of the Fv molecule from a human monoclonal IgM cryogl obulin (Mez) was determined at 2.6 Angstrom resolution. Amino acid sequence s of framework regions (FR) of the Met light (L) and heavy (H) chain variab le domains (VL and VH) are highly similar to their counterparts in another human Fv (Pot) previously subjected to X-ray analysis in our laboratory. As expected, the three-dimensional (3-D) structures of FR are quite similar i n the two proteins, as are four of the six complementarity-determining regi ons (CDRs): CDRs 1 and 2 for both L and H chains. Absence of Pro 95L from t he LCDR3 loop in Met VL (relative to Pot LCDR3) results in compression of t his loop and creates more space in the VL-VH interface. In the two IgMs, HC DR3 conformations differ significantly from all previously defined conforma tions for these loops. Pot has a 12-residue HCDR3 that collapses to fill al l available space in the VL-VH domain interface, resulting in the formation of a relatively flat platform for antigen binding. In Mez, the HCDR3 is tw o residues longer and is comprehensively different. A semi-rigid ascending segment dominated by a Pro-Pro-Tyr sequence protrudes out into solvent. The descending portion has the sequence Gly-Trp-Gly-Gly-Cly, which promotes hi gh local flexibility. This segment folds across the VL-VH domain interface to interact with residues in LCDR3. These features partition the Met active site into two compartments, a large cavity between VL and VH and a smaller cavity lined entirely by constituents of the three heavy chain CDRs. Such an unusual topographical feature indicates why the Met IgM does not bind to the Fc portion of intact human Ige antibodies in immunoassays yet interact s with high avidity with many Fc-derived octapeptides. The cavities are exp ected to be the repositories for the Pc-derived peptides, while the semi-ri gid protrusion of the Mez HCDR3 prevents the close approach of another macr omolecule (e.g. intact IgG) to the active site. (C) 2000 Elsevier Science L td. All rights reserved.