We have determined the structure of murine MHC class II I-A(k) in complex with a naturally processed peptide from hen egg lysozyme (HEL residues 50-62) at 1.9 Å resolution. These results provide a structural basis for the I-A(k) peptide-binding motif. Binding is established by the deep burial of five anchor side chains into specific pockets of the I-A(k) binding groove, with a zen-like fit of an aspartic acid in the P1 pocket. We also show that in the I-A(k) a chain, a bulge occurs in the first strand of the peptide-binding platform, an insertion probably common to all I-A and HLA-DQ alleles. The I-A(k) β chain has a deletion in the helical region adjacent to the P7 pocket and an insertion in the helical region neighboring the P1 pocket. As a result of these structural features, the extended HEL peptide dips low into the center of the I-A(k) groove and reaches toward solvent at its C-terminal end.