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T lymphocyte (CTL) responses against influenza A virus in C57BL/6 mice are dominated by a small number of viral peptides among many that are capable of binding to major histocompatibility complex (MHC) class I molecules. The basis of this limited immune recognition is unknown. Here, we present X-ray structures of MHC class I molecules in complex with two immunodominant epitopes (PA(224-233)/D(b) and PB1(703-711)/K(b)) and one non-immunogenic epitope (HA(468-477)/D(b)) of the influenza A virus. The immunodominant peptides are each characterized by a bulge at the C terminus, lifting P6 and P7 residues out of the MHC groove, presenting featured structural elements to T-cell receptors (TCRs). Immune recognition of PA(224-233)/D(b) will focus largely on the exposed P7 arginine residue. In contrast, the non-immunogenic HA(468-477) peptide lacks prominent features in this C-terminal bulge. In the K(b)-bound PB1(703-711) epitope, the bulge results from a non-canonical binding motif, such that the mode of presentation of this peptide strongly resembles that of D(b)-bound peptides. Given that PA(224-233)/D(b), PB1(703-711)/K(b) and the previously defined NP(366-374)/D(b) epitopes dominate the primary response to influenza A virus in C57BL/6 mice, our findings indicate that residues of the C-terminal bulge are important in selection of the immunodominant CTL repertoire.","bibjson":{"author":[{"initials":"R","lastname":"Meijers","name":"Meijers R"},{"initials":"CC","lastname":"Lai","name":"Lai CC"},{"initials":"Y","lastname":"Yang","name":"Yang Y"},{"initials":"JH","lastname":"Liu","name":"Liu JH"},{"initials":"W","lastname":"Zhong","name":"Zhong W"},{"initials":"JH","lastname":"Wang","name":"Wang JH"},{"initials":"EL","lastname":"Reinherz","name":"Reinherz EL"}],"identifier":[{"id":"10.1016/j.jmb.2004.11.023","type":"doi"},{"id":"15644207","type":"pubmed"}],"issue":["5"],"journal":{"iso_abbreviation":"J. Mol. 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