{"display":true,"structure":{"allele":{"alpha":{"identifier":"uniprot:P01897","locus":"h2-l","match_type":"histo:fuzzy","name":"H2-Ld","slug":"h2_ld","species_stem":"H2"},"beta":{}},"assemblies":{"1":{"assembly_name":"8d5n_1","chains":["C","E","H"],"downloaded_at":"2022-11-09T14:36:10.858679"},"2":{"assembly_name":"8d5n_2","chains":["A","B","F"],"downloaded_at":"2022-11-09T14:36:11.327849"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["F","H"],"match_type":"histo:assign_chains","score":0.98,"sequence":"GGSGGIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM"},"class_i_alpha":{"chains":["C","A"],"match_type":"histo:assign_chains","score":0.97,"sequence":"GPHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYWERITQIAKGQEQWFRVNLRTLLGCYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDGSDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWQSTRGGAS"},"peptide":{"chains":["E","B"],"match_type":"histo:classify_peptide","sequence":"HPGSVNEFDFGCGGSG"}},"chronology":{"deposition_date":"2022-06-05","deposition_year":2022,"release_date":"2022-09-14","release_year":2022,"revision_date":"2022-09-14","revision_year":2022},"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-l","manually_edited":{},"missing_residues":[],"page_title":"8D5N | H2-Ld binding \"HPGSVNEFDFGCGGSG\"","pdb_code":"8d5n","pdb_title":"Crystal structure of ld-hf10","peptide":{"B":{"actual_length":12,"actual_sequence":"HPGSVNEFDFGC","chain_id":"B","features":["missing_end"],"full_length":16,"full_sequence":"HPGSVNEFDFGCGGSG"},"E":{"actual_length":15,"actual_sequence":"HPGSVNEFDFGCGGS","chain_id":"E","features":["missing_end"],"full_length":16,"full_sequence":"HPGSVNEFDFGCGGSG"}},"peptide_length":16,"peptide_length_name":"hexadecamer","peptide_neighbours":{"1":{"neighbours":[{"position":159,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":7,"residue":"TYR"},{"position":167,"residue":"TRP"},{"position":5,"residue":"MET"},{"position":33,"residue":"PHE"},{"position":59,"residue":"TYR"},{"position":63,"residue":"ILE"},{"position":171,"residue":"TYR"},{"position":163,"residue":"GLU"},{"position":66,"residue":"ILE"}],"position":1,"residue":"HIS"},"10":{"neighbours":[{"position":80,"residue":"THR"},{"position":124,"residue":"ILE"},{"position":73,"residue":"TRP"},{"position":146,"residue":"LYS"},{"position":143,"residue":"THR"},{"position":116,"residue":"PHE"},{"position":81,"residue":"LEU"},{"position":147,"residue":"TRP"},{"position":142,"residue":"ILE"},{"position":77,"residue":"ASN"},{"position":123,"residue":"TYR"},{"position":95,"residue":"LEU"}],"position":10,"residue":"PHE"},"11":{"neighbours":[{"position":142,"residue":"ILE"},{"position":77,"residue":"ASN"},{"position":84,"residue":"CYS"},{"position":80,"residue":"THR"},{"position":146,"residue":"LYS"},{"position":143,"residue":"THR"}],"position":11,"residue":"GLY"},"12":{"neighbours":[{"position":81,"residue":"LEU"},{"position":142,"residue":"ILE"},{"position":139,"residue":"ALA"},{"position":80,"residue":"THR"},{"position":84,"residue":"CYS"},{"position":123,"residue":"TYR"},{"position":143,"residue":"THR"}],"position":12,"residue":"CYS"},"13":{"neighbours":[{"position":146,"residue":"LYS"},{"position":142,"residue":"ILE"},{"position":84,"residue":"CYS"}],"position":13,"residue":"GLY"},"14":{"neighbours":[{"position":142,"residue":"ILE"},{"position":146,"residue":"LYS"}],"position":14,"residue":"GLY"},"2":{"neighbours":[{"position":163,"residue":"GLU"},{"position":66,"residue":"ILE"},{"position":159,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":45,"residue":"TYR"},{"position":9,"residue":"GLU"},{"position":63,"residue":"ILE"},{"position":99,"residue":"TYR"}],"position":2,"residue":"PRO"},"3":{"neighbours":[{"position":70,"residue":"GLN"},{"position":99,"residue":"TYR"},{"position":66,"residue":"ILE"},{"position":159,"residue":"TYR"},{"position":97,"residue":"TRP"},{"position":9,"residue":"GLU"}],"position":3,"residue":"GLY"},"4":{"neighbours":[{"position":66,"residue":"ILE"},{"position":70,"residue":"GLN"},{"position":97,"residue":"TRP"}],"position":4,"residue":"SER"},"5":{"neighbours":[{"position":66,"residue":"ILE"},{"position":69,"residue":"GLY"},{"position":65,"residue":"GLN"},{"position":73,"residue":"TRP"},{"position":70,"residue":"GLN"}],"position":5,"residue":"VAL"},"6":{"neighbours":[{"position":74,"residue":"PHE"},{"position":73,"residue":"TRP"},{"position":97,"residue":"TRP"},{"position":156,"residue":"TYR"},{"position":116,"residue":"PHE"},{"position":70,"residue":"GLN"}],"position":6,"residue":"ASN"},"7":{"neighbours":[{"position":155,"residue":"TYR"}],"position":7,"residue":"GLU"},"8":{"neighbours":[{"position":155,"residue":"TYR"},{"position":147,"residue":"TRP"},{"position":73,"residue":"TRP"},{"position":151,"residue":"GLY"},{"position":77,"residue":"ASN"},{"position":150,"residue":"ALA"},{"position":152,"residue":"ALA"}],"position":8,"residue":"PHE"},"9":{"neighbours":[{"position":77,"residue":"ASN"},{"position":76,"residue":"VAL"},{"position":73,"residue":"TRP"},{"position":143,"residue":"THR"},{"position":147,"residue":"TRP"}],"position":9,"residue":"ASP"}},"peptide_sequence":"HPGSVNEFDFGCGGSG","pockets":{"a":{"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a163":{"number":163,"one_letter":"E","three_letter":"GLU"},"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":"I","three_letter":"ILE"},"a66":{"number":66,"one_letter":"I","three_letter":"ILE"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"S","three_letter":"SER"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"Y","three_letter":"TYR"},"a63":{"number":63,"one_letter":"I","three_letter":"ILE"},"a66":{"number":66,"one_letter":"I","three_letter":"ILE"},"a67":{"number":67,"one_letter":"A","three_letter":"ALA"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"Q","three_letter":"GLN"},"a9":{"number":9,"one_letter":"E","three_letter":"GLU"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"Q","three_letter":"GLN"},"a73":{"number":73,"one_letter":"W","three_letter":"TRP"},"a74":{"number":74,"one_letter":"F","three_letter":"PHE"},"a9":{"number":9,"one_letter":"E","three_letter":"GLU"},"a97":{"number":97,"one_letter":"W","three_letter":"TRP"}},"d":{"a114":{"number":114,"one_letter":"E","three_letter":"GLU"},"a155":{"number":155,"one_letter":"Y","three_letter":"TYR"},"a156":{"number":156,"one_letter":"Y","three_letter":"TYR"},"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":"E","three_letter":"GLU"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"A","three_letter":"ALA"},"a156":{"number":156,"one_letter":"Y","three_letter":"TYR"},"a97":{"number":97,"one_letter":"W","three_letter":"TRP"}},"f":{"a116":{"number":116,"one_letter":"F","three_letter":"PHE"},"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":"N","three_letter":"ASN"},"a80":{"number":80,"one_letter":"T","three_letter":"THR"},"a81":{"number":81,"one_letter":"L","three_letter":"LEU"},"a84":{"number":84,"one_letter":"C","three_letter":"CYS"},"a95":{"number":95,"one_letter":"L","three_letter":"LEU"}}},"publication":{"abstract":"Certain CD8 T cell responses are particularly effective at controlling infection, as exemplified by elite control of HIV in individuals harboring HLA-B57. To understand the structural features that contribute to CD8 T cell elite control, we focused on a strongly protective CD8 T cell response directed against a parasite-derived peptide (HF10) presented by an atypical MHC-I molecule, H-2Ld. This response exhibits a focused TCR repertoire dominated by V\u03b22, and a representative TCR (TG6) in complex with Ld-HF10 reveals an unusual structure in which both MHC and TCR contribute extensively to peptide specificity, along with a parallel footprint of TCR on its pMHC ligand. The parallel footprint is a common feature of V\u03b22-containing TCRs and correlates with an unusual V\u03b1-V\u03b2 interface, CDR loop conformations, and V\u03b22-specific germline contacts with peptides. V\u03b22 and Ld may represent \"specialist\" components for antigen recognition that allows for particularly strong and focused T cell responses.","bibjson":{"author":[{"initials":"Y","lastname":"Wang","name":"Wang Y"},{"initials":"A","lastname":"Tsitsiklis","name":"Tsitsiklis A"},{"initials":"S","lastname":"Devoe","name":"Devoe S"},{"initials":"W","lastname":"Gao","name":"Gao W"},{"initials":"HH","lastname":"Chu","name":"Chu HH"},{"initials":"Y","lastname":"Zhang","name":"Zhang Y"},{"initials":"W","lastname":"Li","name":"Li W"},{"initials":"WK","lastname":"Wong","name":"Wong WK"},{"initials":"CM","lastname":"Deane","name":"Deane CM"},{"initials":"D","lastname":"Neau","name":"Neau D"},{"initials":"JE","lastname":"Slansky","name":"Slansky JE"},{"initials":"PG","lastname":"Thomas","name":"Thomas PG"},{"initials":"EA","lastname":"Robey","name":"Robey EA"},{"initials":"S","lastname":"Dai","name":"Dai S"}],"identifier":[{"id":"10.3389/fimmu.2022.847092","type":"doi"},{"id":"35967379","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"Front Immunol","name":""},"pages":["847092"],"title":"Peptide Centric V\u03b2 Specific Germline Contacts Shape a Specialist T Cell Response.","type":"article","url":"https://www.frontiersin.org/articles/10.3389/fimmu.2022.847092/full","volume":["13"],"year":[2022]},"in_pmc":"N","in_pmce":"Y","open_access":"Y"},"resolution":"1.80","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/8d5n"},"rcsb":{"url":"https://www.rcsb.org/structure/8d5n"}},"species":{"common_name":"Mouse","match_type":"histo:assign_species","scientific_name":"Mus musculus","slug":"mus_musculus"},"tcr":null,"title":"H2-Ld binding \"HPGSVNEFDFGCGGSG\" at 1.80Å resolution","unique_chain_count":3}}