{"display":true,"structure":{"allele":{"alpha":{"identifier":"uniprot:P01899","locus":"h2-d","match_type":"histo:fuzzy","name":"H2-Db","slug":"h2_db","species_stem":"H2"},"beta":{}},"assemblies":{"1":{"assembly_name":"3ws3_1","chains":["A","B","E"],"downloaded_at":"2022-11-09T14:35:12.666088"},"2":{"assembly_name":"3ws3_2","chains":["C","D","F"],"downloaded_at":"2022-11-09T14:35:13.075836"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B","D"],"match_type":"histo:assign_chains","score":0.99,"sequence":"MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM"},"class_i_alpha":{"chains":["A","C"],"match_type":"histo:assign_chains","score":1.0,"sequence":"PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRW"},"peptide":{"chains":["E","F"],"match_type":"histo:classify_peptide","sequence":"YQLENYCGL"}},"chronology":{"deposition_date":"2014-02-28","deposition_year":2014,"release_date":"2014-03-26","release_year":2014,"revision_date":"2018-02-07","revision_year":2018},"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":"h2-d","manually_edited":{},"missing_residues":[],"page_title":"3WS3 | H2-Db binding \"YQLENYCGL\"","pdb_code":"3ws3","pdb_title":"Crystal structure of h-2d in complex with an insulin derived peptide","peptide":{"E":{"actual_length":9,"actual_sequence":"YQLENYCGL","chain_id":"E","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"YQLENYCGL"},"F":{"actual_length":9,"actual_sequence":"YQLENYCGL","chain_id":"F","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"YQLENYCGL"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":183,"residue":"TYR"},{"position":31,"residue":"TYR"},{"position":195,"residue":"TYR"},{"position":57,"residue":"PHE"},{"position":86,"residue":"ARG"},{"position":83,"residue":"TYR"},{"position":187,"residue":"GLU"},{"position":29,"residue":"MET"},{"position":90,"residue":"LYS"},{"position":191,"residue":"TRP"},{"position":87,"residue":"GLU"}],"position":1,"residue":"TYR"},"2":{"neighbours":[{"position":33,"residue":"GLU"},{"position":48,"residue":"SER"},{"position":31,"residue":"TYR"},{"position":90,"residue":"LYS"},{"position":87,"residue":"GLU"},{"position":91,"residue":"ALA"},{"position":183,"residue":"TYR"},{"position":46,"residue":"TYR"},{"position":69,"residue":"TYR"},{"position":94,"residue":"GLN"}],"position":2,"residue":"GLN"},"3":{"neighbours":[{"position":138,"residue":"LEU"},{"position":94,"residue":"GLN"},{"position":121,"residue":"GLN"},{"position":179,"residue":"HIS"},{"position":123,"residue":"SER"},{"position":90,"residue":"LYS"},{"position":183,"residue":"TYR"},{"position":180,"residue":"TYR"}],"position":3,"residue":"LEU"},"4":{"neighbours":[{"position":179,"residue":"HIS"},{"position":90,"residue":"LYS"},{"position":180,"residue":"TYR"},{"position":94,"residue":"GLN"}],"position":4,"residue":"GLU"},"5":{"neighbours":[{"position":140,"residue":"PHE"},{"position":179,"residue":"HIS"},{"position":94,"residue":"GLN"},{"position":33,"residue":"GLU"},{"position":121,"residue":"GLN"},{"position":180,"residue":"TYR"},{"position":98,"residue":"PHE"},{"position":97,"residue":"TRP"}],"position":5,"residue":"ASN"},"6":{"neighbours":[{"position":180,"residue":"TYR"},{"position":97,"residue":"TRP"},{"position":175,"residue":"GLY"},{"position":174,"residue":"SER"},{"position":176,"residue":"ALA"},{"position":179,"residue":"HIS"}],"position":6,"residue":"TYR"},"7":{"neighbours":[{"position":180,"residue":"TYR"},{"position":171,"residue":"TRP"},{"position":97,"residue":"TRP"},{"position":174,"residue":"SER"},{"position":176,"residue":"ALA"}],"position":7,"residue":"CYS"},"8":{"neighbours":[{"position":171,"residue":"TRP"},{"position":97,"residue":"TRP"},{"position":167,"residue":"THR"},{"position":101,"residue":"SER"},{"position":170,"residue":"LYS"}],"position":8,"residue":"GLY"},"9":{"neighbours":[{"position":170,"residue":"LYS"},{"position":171,"residue":"TRP"},{"position":108,"residue":"TYR"},{"position":97,"residue":"TRP"},{"position":119,"residue":"LEU"},{"position":101,"residue":"SER"},{"position":167,"residue":"THR"},{"position":105,"residue":"LEU"},{"position":104,"residue":"ASN"},{"position":140,"residue":"PHE"},{"position":147,"residue":"TYR"},{"position":148,"residue":"ILE"}],"position":9,"residue":"LEU"}},"peptide_sequence":"YQLENYCGL","pockets":{"a":{"a159":{"number":159,"one_letter":"L","three_letter":"LEU"},"a163":{"number":163,"one_letter":"C","three_letter":"CYS"},"a167":{"number":167,"one_letter":"L","three_letter":"LEU"},"a171":{"number":171,"one_letter":"L","three_letter":"LEU"},"a5":{"number":5,"one_letter":"R","three_letter":"ARG"},"a59":{"number":59,"one_letter":"W","three_letter":"TRP"},"a63":{"number":63,"one_letter":"T","three_letter":"THR"},"a66":{"number":66,"one_letter":"A","three_letter":"ALA"},"a7":{"number":7,"one_letter":"F","three_letter":"PHE"}},"b":{"a24":{"number":24,"one_letter":"V","three_letter":"VAL"},"a34":{"number":34,"one_letter":"R","three_letter":"ARG"},"a45":{"number":45,"one_letter":"E","three_letter":"GLU"},"a63":{"number":63,"one_letter":"T","three_letter":"THR"},"a66":{"number":66,"one_letter":"A","three_letter":"ALA"},"a67":{"number":67,"one_letter":"K","three_letter":"LYS"},"a7":{"number":7,"one_letter":"F","three_letter":"PHE"},"a70":{"number":70,"one_letter":"E","three_letter":"GLU"},"a9":{"number":9,"one_letter":"T","three_letter":"THR"},"a99":{"number":99,"one_letter":"G","three_letter":"GLY"}},"c":{"a70":{"number":70,"one_letter":"E","three_letter":"GLU"},"a73":{"number":73,"one_letter":"F","three_letter":"PHE"},"a74":{"number":74,"one_letter":"R","three_letter":"ARG"},"a9":{"number":9,"one_letter":"T","three_letter":"THR"},"a97":{"number":97,"one_letter":"M","three_letter":"MET"}},"d":{"a114":{"number":114,"one_letter":"Q","three_letter":"GLN"},"a155":{"number":155,"one_letter":"Y","three_letter":"TYR"},"a156":{"number":156,"one_letter":"K","three_letter":"LYS"},"a159":{"number":159,"one_letter":"L","three_letter":"LEU"},"a160":{"number":160,"one_letter":"E","three_letter":"GLU"},"a99":{"number":99,"one_letter":"G","three_letter":"GLY"}},"e":{"a114":{"number":114,"one_letter":"Q","three_letter":"GLN"},"a147":{"number":147,"one_letter":"E","three_letter":"GLU"},"a152":{"number":152,"one_letter":"A","three_letter":"ALA"},"a156":{"number":156,"one_letter":"K","three_letter":"LYS"},"a97":{"number":97,"one_letter":"M","three_letter":"MET"}},"f":{"a116":{"number":116,"one_letter":"A","three_letter":"ALA"},"a123":{"number":123,"one_letter":"I","three_letter":"ILE"},"a143":{"number":143,"one_letter":"R","three_letter":"ARG"},"a146":{"number":146,"one_letter":"W","three_letter":"TRP"},"a147":{"number":147,"one_letter":"E","three_letter":"GLU"},"a77":{"number":77,"one_letter":"L","three_letter":"LEU"},"a80":{"number":80,"one_letter":"L","three_letter":"LEU"},"a81":{"number":81,"one_letter":"L","three_letter":"LEU"},"a84":{"number":84,"one_letter":"Y","three_letter":"TYR"},"a95":{"number":95,"one_letter":"Q","three_letter":"GLN"}}},"publication":{"abstract":"Self-reactive T cells must escape thymic negative selection to mediate pathogenic autoimmunity. In the NOD mouse model of autoimmune diabetes, several \u03b2 cell-cytotoxic CD8 T cell populations are known, with the most aggressive of these represented by AI4, a T cell clone with promiscuous Ag-recognition characteristics. We identified a long-elusive \u03b2 cell-specific ligand for AI4 as an unusually short H-2D(b)-binding 7-mer peptide lacking a C-terminal anchor residue and derived from the insulin A chain (InsA14-20). Crystallography reveals that compensatory mechanisms permit peptides lacking a C-terminal anchor to bind sufficiently to the MHC to enable destructive T cell responses, yet allow cognate T cells to avoid negative selection. InsA14-20 shares two solvent-exposed residues with previously identified AI4 ligands, providing a structural explanation for AI4's promiscuity. Detection of AI4-like T cells, using mimotopes of InsA14-20 with improved H-2D(b)-binding characteristics, establishes the AI4-like T cell population as a consistent feature of the islet infiltrates of NOD mice. Our work establishes undersized peptides as previously unrecognized targets of autoreactive CD8 T cells and presents a strategy for their further exploration as Ags in autoimmune disease.","bibjson":{"author":[{"initials":"D","lastname":"Lamont","name":"Lamont D"},{"initials":"G","lastname":"Mukherjee","name":"Mukherjee G"},{"initials":"PR","lastname":"Kumar","name":"Kumar PR"},{"initials":"D","lastname":"Samanta","name":"Samanta D"},{"initials":"CG","lastname":"McPhee","name":"McPhee CG"},{"initials":"TW","lastname":"Kay","name":"Kay TW"},{"initials":"SC","lastname":"Almo","name":"Almo SC"},{"initials":"TP","lastname":"DiLorenzo","name":"DiLorenzo TP"},{"initials":"DV","lastname":"Serreze","name":"Serreze DV"}],"identifier":[{"id":"10.4049/jimmunol.1400997","type":"doi"},{"id":"25063871","type":"pubmed"}],"issue":["5"],"journal":{"iso_abbreviation":"J. Immunol.","name":""},"pages":["2135-46"],"title":"Compensatory mechanisms allow undersized anchor-deficient class I MHC ligands to mediate pathogenic autoreactive T cell responses.","type":"article","url":"http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1400997","volume":["193"],"year":[2014]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"2.33","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/3ws3"},"rcsb":{"url":"https://www.rcsb.org/structure/3ws3"}},"species":{"common_name":"Mouse","match_type":"histo:assign_species","scientific_name":"Mus musculus","slug":"mus_musculus"},"tcr":null,"title":"H2-Db binding \"YQLENYCGL\" at 2.33Å resolution","unique_chain_count":3}}