Cytotoxic T lymphocytes (CTL) specific for influenza A virus were prepared from 15 donors. Those with HLA-A2 recognized autologous or HLA-A2-matched Blymphoblastoid cells in the presence of synthetic peptide representing residues 55-73 or 56-68 of the virus matrix protein sequence. Influenza A virus-specific CTL from donors without HLA-A2 or with an HLA-A2 variant type failed to respond to this peptide. CTL lines specific for HLA-A2 plus peptide did not lyse peptide-treated target cells from HLA-A2 variant donors. They also failed to lyse peptide-treated cells with point mutations that had been inserted into HLA-A2 at positions 62-63, 66, 152, and 156 and, in some instances, mutations at positions 9 and 70. CTL lysed peptide-treated target cells with mutations in HLA-A2 at positions 43, 74, and 107. The results imply that this defined peptide epitope therefore interacts with HLA-A2 in the binding groove so that the long a-helices of HLA-A2 make important contact with the peptide at positions 66, 152, and 156. Different amino acids at position 9, which is in the floor of the peptide binding groove of HLA-A2 and the closely related position 70, modulate the peptide interaction so that some T-cell clones react and some do not.Influenza virus-specific cytotoxic T lymphocytes (CTL) recognize both external and internal proteins of virus on infected cells (1-4). A major component of this response is directed toward the nucleoprotein in mice (2, 3) and nucleoprotein and the matrix protein in humans (4). Class I molecules of the major histocompatibility complex (MHC) were shown to play a major role in this process, first by the demonstration of MHC restriction, where CTL recognize only histocompatible infected target cells (5), and more recently by the finding that MHC type determines, directly or indirectly, the epitope recognized by CTL (6-8). The mechanism underlying these effects became clearer when it was found that influenza virus-specific CTL reacted with short synthetic peptides based on virus protein sequences when presented by uninfected target cells of the appropriate MHC type (9). This implied that virus proteins were processed to peptide fragments that bound to MHC molecules prior to recognition by CTL. The crystal structure of HLA-A2 revealed unidentified electron density, probably peptide, present in a pocket on the surface of the molecule (10). This groove was formed by two a-helices lying across an eightstranded P-sheet. Nearly all of the polymorphic amino acid residues in the class I molecule were located around this groove (11). Thus, it is likely that the peptide 55-73 from influenza virus matrix protein, which has been shown to be recognized by CTL in association with HLA-A2 (8), binds in this groove.The experiments described here test the effects of natural and deliberately introduced mutations in HLA-A2 on recognition of the matrix peptide by CTL. It is shown that mutations in HLA-A2 located around the groove impaired recognition but that there were variable effects with different CTL clone...