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peptides are loaded onto class I MHC molecules in the endoplasmic reticulum (ER) by a complex consisting of the MHC class I heavy chain, beta(2)-microglobulin, calreticulin, tapasin, Erp57 (ER60) and the transporter associated with antigen processing (TAP). While most mammalian species transport these peptides into the ER via a single allele of TAP, rats have evolved different TAPs, TAP-A and TAP-B, that are present in different inbred strains. Each TAP delivers a different spectrum of peptides and is associated genetically with distinct subsets of MHC class Ia alleles, but the molecular basis for the conservation (or co-evolution) of the two transporter alleles is unknown. We have determined the crystal structures of a representative of each MHC subset, viz RT1-A(a) and RT1-A1(c), in association with high-affinity nonamer peptides. The structures reveal how the chemical properties of the two different rat MHC F-pockets match those of the corresponding C termini of the peptides, corroborating biochemical data on the rates of peptide-MHC complex assembly. An unusual sequence in RT1-A1(c) leads to a major deviation from the highly conserved beta(3)/alpha(1) loop (residues 40-59) conformation in mouse and human MHC class I structures. This loop change contributes to profound changes in the shape of the A-pocket in the peptide-binding groove and may explain the function of RT1-A1(c) as an inhibitory natural killer cell ligand.","bibjson":{"author":[{"initials":"MG","lastname":"Rudolph","name":"Rudolph MG"},{"initials":"J","lastname":"Stevens","name":"Stevens J"},{"initials":"JA","lastname":"Speir","name":"Speir JA"},{"initials":"J","lastname":"Trowsdale","name":"Trowsdale J"},{"initials":"GW","lastname":"Butcher","name":"Butcher GW"},{"initials":"E","lastname":"Joly","name":"Joly E"},{"initials":"IA","lastname":"Wilson","name":"Wilson IA"}],"identifier":[{"id":"10.1016/s0022-2836(02)01095-1","type":"doi"},{"id":"12470953","type":"pubmed"}],"issue":["5"],"journal":{"iso_abbreviation":"J. Mol. 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