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N and C termini of peptides presented by major histocompatibility complex (MHC) class I molecules are held within the peptide binding groove by a network of hydrogen bonds to conserved MHC residues. However, the published structure of the human allele HLA-B*3501 complexed with the nef octa-peptide VPLRPMTY, revealed non-standard positioning for both peptide termini. To investigate whether these deviations are indeed related to the length of the nef-peptide, we have determined the structure of HLA-B*3501 presenting a nona-peptide to 2.5 A resolution. A comparison of HLA-B*3501/peptide complexes with structures of other HLA molecules exhibits allele-specific properties of HLA-B*3501, as well as peptide-induced structural changes. Independent of the length of the bound peptide, HLA-B*3501 positions the peptide C terminus significantly closer to the alpha1-helix and nearer to the A pocket than observed for other HLA class I/peptide complexes. This reorientation is accompanied by a shift within the N-terminal part of the alpha2-helix towards the middle of the binding groove. Due to the short distance between the N and C termini, the nona-peptide is compressed and forced to zig-zag vertically within the binding groove. Its conformation rather resembles that of a deca-peptide than of other nona-peptides bound to class I molecules. Superposition of both HLA-B*3501/peptide complexes additionally reveals a significant, peptide-dependent deviation between the N-terminal parts of the alpha1-helices which might be due to different positioning of the peptide N termini. Taken together, these data illustrate the strong interdependence between the HLA class I molecule and the bound peptide.","bibjson":{"author":[{"initials":"R","lastname":"Menssen","name":"Menssen R"},{"initials":"P","lastname":"Orth","name":"Orth P"},{"initials":"A","lastname":"Ziegler","name":"Ziegler A"},{"initials":"W","lastname":"Saenger","name":"Saenger W"}],"identifier":[{"id":"10.1006/jmbi.1998.2363","type":"doi"},{"id":"9878435","type":"pubmed"}],"issue":["2"],"journal":{"iso_abbreviation":"J. Mol. Biol.","name":""},"pages":["645-53"],"title":"Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S0022283698923634","volume":["285"],"year":[1999]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"3.20","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/1a9b"},"rcsb":{"url":"https://www.rcsb.org/structure/1a9b"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-B*35:01 binding \"LPPLDITPY\" at 3.20Å resolution","unique_chain_count":3}}