{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA34423","locus":"hla-b","match_type":"histo:exact","name":"HLA-B*35:01","slug":"hla_b_35_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"1xh3_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:29:13.537793"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":1.0,"sequence":"IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["A"],"match_type":"histo:assign_chains","score":0.91,"sequence":"GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYWDRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQRADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP"},"peptide":{"chains":["C"],"match_type":"histo:classify_peptide","sequence":"LPAVVGLSPGEQEY"}},"chronology":{"deposition_date":"2004-09-17","deposition_year":2004,"release_date":"2004-11-23","release_year":2004,"revision_date":"2011-07-13","revision_year":2011},"class":"class_i","classical":true,"complex_type":"class_i_with_peptide","components":["class_i_alpha","beta2m","peptide"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"hla-b","manually_edited":{},"missing_residues":[],"page_title":"1XH3 | HLA-B*35:01 binding \"LPAVVGLSPGEQEY\"","pdb_code":"1xh3","pdb_title":"Conformational restraints and flexibility of 14-meric peptides in complex with HLA-B*3501.","peptide":{"C":{"actual_length":14,"actual_sequence":"LPAVVGLSPGEQEY","chain_id":"C","features":["correct_sequence_and_length"],"full_length":14,"full_sequence":"LPAVVGLSPGEQEY"}},"peptide_length":14,"peptide_length_name":"tetradecamer","peptide_neighbours":{"1":{"neighbours":[{"position":59,"residue":"TYR"},{"position":33,"residue":"PHE"},{"position":5,"residue":"MET"},{"position":159,"residue":"TYR"},{"position":171,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":7,"residue":"TYR"},{"position":167,"residue":"TRP"},{"position":163,"residue":"LEU"},{"position":63,"residue":"ASN"}],"position":1,"residue":"LEU"},"11":{"neighbours":[{"position":147,"residue":"TRP"},{"position":150,"residue":"ALA"},{"position":152,"residue":"VAL"}],"position":11,"residue":"GLU"},"12":{"neighbours":[{"position":69,"residue":"THR"},{"position":73,"residue":"THR"},{"position":77,"residue":"SER"},{"position":147,"residue":"TRP"},{"position":70,"residue":"ASN"}],"position":12,"residue":"GLN"},"13":{"neighbours":[{"position":146,"residue":"LYS"},{"position":73,"residue":"THR"},{"position":77,"residue":"SER"},{"position":147,"residue":"TRP"},{"position":80,"residue":"ASN"},{"position":76,"residue":"GLU"}],"position":13,"residue":"GLU"},"14":{"neighbours":[{"position":143,"residue":"THR"},{"position":97,"residue":"ARG"},{"position":80,"residue":"ASN"},{"position":116,"residue":"SER"},{"position":81,"residue":"LEU"},{"position":123,"residue":"TYR"},{"position":77,"residue":"SER"},{"position":124,"residue":"ILE"},{"position":147,"residue":"TRP"},{"position":84,"residue":"TYR"},{"position":146,"residue":"LYS"},{"position":95,"residue":"ILE"},{"position":142,"residue":"ILE"},{"position":74,"residue":"TYR"},{"position":96,"residue":"GLN"}],"position":14,"residue":"TYR"},"2":{"neighbours":[{"position":159,"residue":"TYR"},{"position":63,"residue":"ASN"},{"position":99,"residue":"TYR"},{"position":66,"residue":"ILE"},{"position":67,"residue":"PHE"},{"position":9,"residue":"TYR"},{"position":7,"residue":"TYR"}],"position":2,"residue":"PRO"},"3":{"neighbours":[{"position":9,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":156,"residue":"LEU"},{"position":66,"residue":"ILE"},{"position":99,"residue":"TYR"}],"position":3,"residue":"ALA"},"4":{"neighbours":[{"position":66,"residue":"ILE"},{"position":155,"residue":"GLN"},{"position":62,"residue":"ARG"}],"position":4,"residue":"VAL"},"5":{"neighbours":[{"position":156,"residue":"LEU"},{"position":152,"residue":"VAL"},{"position":155,"residue":"GLN"}],"position":5,"residue":"VAL"},"6":{"neighbours":[{"position":155,"residue":"GLN"}],"position":6,"residue":"GLY"},"7":{"neighbours":[{"position":150,"residue":"ALA"},{"position":155,"residue":"GLN"}],"position":7,"residue":"LEU"},"9":{"neighbours":[{"position":73,"residue":"THR"},{"position":69,"residue":"THR"}],"position":9,"residue":"PRO"}},"peptide_sequence":"LPAVVGLSPGEQEY","pockets":{"a":{"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a163":{"number":163,"one_letter":"L","three_letter":"LEU"},"a167":{"number":167,"one_letter":"W","three_letter":"TRP"},"a171":{"number":171,"one_letter":"Y","three_letter":"TYR"},"a5":{"number":5,"one_letter":"M","three_letter":"MET"},"a59":{"number":59,"one_letter":"Y","three_letter":"TYR"},"a63":{"number":63,"one_letter":"N","three_letter":"ASN"},"a66":{"number":66,"one_letter":"I","three_letter":"ILE"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"A","three_letter":"ALA"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"T","three_letter":"THR"},"a63":{"number":63,"one_letter":"N","three_letter":"ASN"},"a66":{"number":66,"one_letter":"I","three_letter":"ILE"},"a67":{"number":67,"one_letter":"F","three_letter":"PHE"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"a9":{"number":9,"one_letter":"Y","three_letter":"TYR"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"a73":{"number":73,"one_letter":"T","three_letter":"THR"},"a74":{"number":74,"one_letter":"Y","three_letter":"TYR"},"a9":{"number":9,"one_letter":"Y","three_letter":"TYR"},"a97":{"number":97,"one_letter":"R","three_letter":"ARG"}},"d":{"a114":{"number":114,"one_letter":"D","three_letter":"ASP"},"a155":{"number":155,"one_letter":"Q","three_letter":"GLN"},"a156":{"number":156,"one_letter":"L","three_letter":"LEU"},"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a160":{"number":160,"one_letter":"L","three_letter":"LEU"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"e":{"a114":{"number":114,"one_letter":"D","three_letter":"ASP"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"V","three_letter":"VAL"},"a156":{"number":156,"one_letter":"L","three_letter":"LEU"},"a97":{"number":97,"one_letter":"R","three_letter":"ARG"}},"f":{"a116":{"number":116,"one_letter":"S","three_letter":"SER"},"a123":{"number":123,"one_letter":"Y","three_letter":"TYR"},"a143":{"number":143,"one_letter":"T","three_letter":"THR"},"a146":{"number":146,"one_letter":"K","three_letter":"LYS"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a77":{"number":77,"one_letter":"S","three_letter":"SER"},"a80":{"number":80,"one_letter":"N","three_letter":"ASN"},"a81":{"number":81,"one_letter":"L","three_letter":"LEU"},"a84":{"number":84,"one_letter":"Y","three_letter":"TYR"},"a95":{"number":95,"one_letter":"I","three_letter":"ILE"}}},"publication":{"abstract":"Human HLA-B*3501 binds an antigenic peptide of 14-aa length derived from an alternative reading frame of M-CSF with high affinity. Due to its extraordinary length, the exact HLA binding mode was unpredictable. The crystal structure of HLA-B*3501 at 1.5 A shows that the N and C termini of the peptide are embedded in the A and F pockets, respectively, similar to a peptide of normal length. The central part of the 14-meric peptide bulges flexibly out of the groove. Two variants of the alternative reading frame of M-CSF peptide substituted at P2 or P2 and P9 with Ala display weak or no T cell activation. Their structure differs mainly in flexibility and conformation from the agonistic peptide. Moreover, the variants induce subtle changes of MHC alpha-helical regions implicated as critical for TCR contact. The TCR specifically recognizing this peptide/MHC complex exhibits CDR3 length within the normal range, suggesting major conformational adaptations of this receptor upon peptide/MHC binding. Thus, the potential antigenic repertoire recognizable by CTLs is larger than currently thought.","bibjson":{"author":[{"initials":"M","lastname":"Probst-Kepper","name":"Probst-Kepper M"},{"initials":"HJ","lastname":"Hecht","name":"Hecht HJ"},{"initials":"H","lastname":"Herrmann","name":"Herrmann H"},{"initials":"V","lastname":"Janke","name":"Janke V"},{"initials":"F","lastname":"Ocklenburg","name":"Ocklenburg F"},{"initials":"J","lastname":"Klempnauer","name":"Klempnauer J"},{"initials":"BJ","lastname":"van den Eynde","name":"van den Eynde BJ"},{"initials":"S","lastname":"Weiss","name":"Weiss S"}],"identifier":[{"id":"10.4049/jimmunol.173.9.5610","type":"doi"},{"id":"15494511","type":"pubmed"}],"issue":["9"],"journal":{"iso_abbreviation":"J. Immunol.","name":""},"pages":["5610-6"],"title":"Conformational restraints and flexibility of 14-meric peptides in complex with HLA-B*3501.","type":"article","url":"http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.173.9.5610","volume":["173"],"year":[2004]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"1.48","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/1xh3"},"rcsb":{"url":"https://www.rcsb.org/structure/1xh3"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-B*35:01 binding \"LPAVVGLSPGEQEY\" at 1.48Å resolution","unique_chain_count":3}}