{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA35266","locus":"hla-a","match_type":"histo:exact","name":"HLA-A*02:01","slug":"hla_a_02_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"6rp9_1","chains":["A","B","C","D","E"],"downloaded_at":"2022-11-09T14:39:47.406870"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B","G"],"match_type":"histo:assign_chains","score":0.99,"sequence":"MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["A","F"],"match_type":"histo:assign_chains","score":1.0,"sequence":"MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP"},"peptide":{"chains":["C","H"],"match_type":"histo:classify_peptide","sequence":"SLLMWITQV"},"tcr_alpha":{"chains":["D"],"match_type":"stcrdab","sequence":"MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCALTRGPGNQFYFGTGTSLTVIPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS","subgroup":"TRAV12"},"tcr_beta":{"chains":["E"],"match_type":"stcrdab","sequence":"MGAGVSQSPRYKVTKRGQDVALRCDPISGHVSLYWYRQALGQGPEFLTYFNYEAQQDKSGLPNDRFSAERPEGSISTLTIQRTEQRDSAMYRCASSSPGGVSTEAFFGQGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD","subgroup":"TRBV7"}},"chronology":{"deposition_date":"2019-05-14","deposition_year":2019,"release_date":"2020-01-15","release_year":2020,"revision_date":"2020-04-08","revision_year":2020},"class":"class_i","classical":true,"complex_type":"class_i_with_peptide_and_alpha_beta_tcr","components":["class_i_alpha","beta2m","peptide","tcr_alpha","tcr_beta"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"hla-a","manually_edited":{},"missing_residues":[],"page_title":"6RP9 | HLA-A*02:01 presenting \"SLLMWITQV\" to Alpha/Beta T cell receptor","pdb_code":"6rp9","pdb_title":"Crystal structure of the t-cell receptor nye_s3 bound to hla a2*01-SLLMWITQV","peptide":{"C":{"actual_length":9,"actual_sequence":"SLLMWITQV","chain_id":"C","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"SLLMWITQV"},"H":{"actual_length":9,"actual_sequence":"SLLMWITQV","chain_id":"H","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"SLLMWITQV"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":59,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":171,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":5,"residue":"MET"},{"position":159,"residue":"TYR"},{"position":167,"residue":"TRP"},{"position":63,"residue":"GLU"},{"position":33,"residue":"PHE"}],"position":1,"residue":"SER"},"2":{"neighbours":[{"position":63,"residue":"GLU"},{"position":67,"residue":"VAL"},{"position":159,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":9,"residue":"PHE"},{"position":45,"residue":"MET"},{"position":70,"residue":"HIS"},{"position":99,"residue":"TYR"},{"position":66,"residue":"LYS"}],"position":2,"residue":"LEU"},"3":{"neighbours":[{"position":70,"residue":"HIS"},{"position":159,"residue":"TYR"},{"position":156,"residue":"LEU"},{"position":97,"residue":"ARG"},{"position":99,"residue":"TYR"},{"position":66,"residue":"LYS"}],"position":3,"residue":"LEU"},"4":{"neighbours":[{"position":65,"residue":"ARG"},{"position":66,"residue":"LYS"},{"position":69,"residue":"ALA"},{"position":155,"residue":"GLN"}],"position":4,"residue":"MET"},"5":{"neighbours":[{"position":74,"residue":"HIS"},{"position":114,"residue":"HIS"},{"position":156,"residue":"LEU"},{"position":73,"residue":"THR"},{"position":97,"residue":"ARG"},{"position":147,"residue":"TRP"},{"position":66,"residue":"LYS"},{"position":116,"residue":"TYR"},{"position":69,"residue":"ALA"},{"position":152,"residue":"VAL"},{"position":70,"residue":"HIS"},{"position":155,"residue":"GLN"}],"position":5,"residue":"TRP"},"6":{"neighbours":[{"position":69,"residue":"ALA"},{"position":73,"residue":"THR"}],"position":6,"residue":"ILE"},"7":{"neighbours":[{"position":147,"residue":"TRP"},{"position":73,"residue":"THR"},{"position":116,"residue":"TYR"},{"position":77,"residue":"ASP"},{"position":152,"residue":"VAL"},{"position":155,"residue":"GLN"}],"position":7,"residue":"THR"},"8":{"neighbours":[{"position":147,"residue":"TRP"},{"position":73,"residue":"THR"},{"position":77,"residue":"ASP"},{"position":76,"residue":"VAL"},{"position":143,"residue":"THR"}],"position":8,"residue":"GLN"},"9":{"neighbours":[{"position":146,"residue":"LYS"},{"position":123,"residue":"TYR"},{"position":143,"residue":"THR"},{"position":80,"residue":"THR"},{"position":116,"residue":"TYR"},{"position":81,"residue":"LEU"},{"position":147,"residue":"TRP"},{"position":84,"residue":"TYR"},{"position":77,"residue":"ASP"}],"position":9,"residue":"VAL"}},"peptide_sequence":"SLLMWITQV","pockets":{"a":{"a159":{"number":159,"one_letter":"A","three_letter":"ALA"},"a163":{"number":163,"one_letter":"G","three_letter":"GLY"},"a167":{"number":167,"one_letter":"E","three_letter":"GLU"},"a171":{"number":171,"one_letter":"R","three_letter":"ARG"},"a5":{"number":5,"one_letter":"S","three_letter":"SER"},"a59":{"number":59,"one_letter":"E","three_letter":"GLU"},"a63":{"number":63,"one_letter":"G","three_letter":"GLY"},"a66":{"number":66,"one_letter":"R","three_letter":"ARG"},"a7":{"number":7,"one_letter":"R","three_letter":"ARG"}},"b":{"a24":{"number":24,"one_letter":"I","three_letter":"ILE"},"a34":{"number":34,"one_letter":"F","three_letter":"PHE"},"a45":{"number":45,"one_letter":"R","three_letter":"ARG"},"a63":{"number":63,"one_letter":"G","three_letter":"GLY"},"a66":{"number":66,"one_letter":"R","three_letter":"ARG"},"a67":{"number":67,"one_letter":"K","three_letter":"LYS"},"a7":{"number":7,"one_letter":"R","three_letter":"ARG"},"a70":{"number":70,"one_letter":"A","three_letter":"ALA"},"a9":{"number":9,"one_letter":"F","three_letter":"PHE"},"a99":{"number":99,"one_letter":"M","three_letter":"MET"}},"c":{"a70":{"number":70,"one_letter":"A","three_letter":"ALA"},"a73":{"number":73,"one_letter":"Q","three_letter":"GLN"},"a74":{"number":74,"one_letter":"T","three_letter":"THR"},"a9":{"number":9,"one_letter":"F","three_letter":"PHE"},"a97":{"number":97,"one_letter":"Q","three_letter":"GLN"}},"d":{"a114":{"number":114,"one_letter":"Y","three_letter":"TYR"},"a155":{"number":155,"one_letter":"E","three_letter":"GLU"},"a156":{"number":156,"one_letter":"Q","three_letter":"GLN"},"a159":{"number":159,"one_letter":"A","three_letter":"ALA"},"a160":{"number":160,"one_letter":"Y","three_letter":"TYR"},"a99":{"number":99,"one_letter":"M","three_letter":"MET"}},"e":{"a114":{"number":114,"one_letter":"Y","three_letter":"TYR"},"a147":{"number":147,"one_letter":"K","three_letter":"LYS"},"a152":{"number":152,"one_letter":"H","three_letter":"HIS"},"a156":{"number":156,"one_letter":"Q","three_letter":"GLN"},"a97":{"number":97,"one_letter":"Q","three_letter":"GLN"}},"f":{"a116":{"number":116,"one_letter":"Q","three_letter":"GLN"},"a123":{"number":123,"one_letter":"D","three_letter":"ASP"},"a143":{"number":143,"one_letter":"T","three_letter":"THR"},"a146":{"number":146,"one_letter":"H","three_letter":"HIS"},"a147":{"number":147,"one_letter":"K","three_letter":"LYS"},"a77":{"number":77,"one_letter":"V","three_letter":"VAL"},"a80":{"number":80,"one_letter":"G","three_letter":"GLY"},"a81":{"number":81,"one_letter":"T","three_letter":"THR"},"a84":{"number":84,"one_letter":"G","three_letter":"GLY"},"a95":{"number":95,"one_letter":"T","three_letter":"THR"}}},"publication":{"abstract":"The molecular rules driving TCR cross-reactivity are poorly understood and, consequently, it is unclear the extent to which TCRs targeting the same Ag recognize the same off-target peptides. We determined TCR-peptide-HLA crystal structures and, using a single-chain peptide-HLA phage library, we generated peptide specificity profiles for three newly identified human TCRs specific for the cancer testis Ag NY-ESO-1157-165-HLA-A2. Two TCRs engaged the same central peptide feature, although were more permissive at peripheral peptide positions and, accordingly, possessed partially overlapping peptide specificity profiles. The third TCR engaged a flipped peptide conformation, leading to the recognition of off-target peptides sharing little similarity with the cognate peptide. These data show that TCRs specific for a cognate peptide recognize discrete peptide repertoires and reconciles how an individual's limited TCR repertoire following negative selection in the thymus is able to recognize a vastly larger antigenic pool.","bibjson":{"author":[{"initials":"CH","lastname":"Coles","name":"Coles CH"},{"initials":"RM","lastname":"Mulvaney","name":"Mulvaney RM"},{"initials":"S","lastname":"Malla","name":"Malla S"},{"initials":"A","lastname":"Walker","name":"Walker A"},{"initials":"KJ","lastname":"Smith","name":"Smith KJ"},{"initials":"A","lastname":"Lloyd","name":"Lloyd A"},{"initials":"KL","lastname":"Lowe","name":"Lowe KL"},{"initials":"ML","lastname":"McCully","name":"McCully ML"},{"initials":"R","lastname":"Martinez Hague","name":"Martinez Hague R"},{"initials":"M","lastname":"Aleksic","name":"Aleksic M"},{"initials":"J","lastname":"Harper","name":"Harper J"},{"initials":"SJ","lastname":"Paston","name":"Paston SJ"},{"initials":"Z","lastname":"Donnellan","name":"Donnellan Z"},{"initials":"F","lastname":"Chester","name":"Chester F"},{"initials":"K","lastname":"Wiederhold","name":"Wiederhold K"},{"initials":"RA","lastname":"Robinson","name":"Robinson RA"},{"initials":"A","lastname":"Knox","name":"Knox A"},{"initials":"AR","lastname":"Stacey","name":"Stacey AR"},{"initials":"J","lastname":"Dukes","name":"Dukes J"},{"initials":"E","lastname":"Baston","name":"Baston E"},{"initials":"S","lastname":"Griffin","name":"Griffin S"},{"initials":"BK","lastname":"Jakobsen","name":"Jakobsen BK"},{"initials":"A","lastname":"Vuidepot","name":"Vuidepot A"},{"initials":"S","lastname":"Harper","name":"Harper S"}],"identifier":[{"id":"10.4049/jimmunol.1900915","type":"doi"},{"id":"32102902","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"J. Immunol.","name":""},"pages":[null],"title":"TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex.","type":"article","url":"http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1900915","volume":[null],"year":[2020]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"3.12","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6rp9"},"rcsb":{"url":"https://www.rcsb.org/structure/6rp9"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=6rp9"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":{"alpha":{"chains":["D"],"subgroup":"TRAV12"},"beta":{"chains":["E"],"subgroup":"TRBV7"},"mhc_type":"class_i","pdb_code":"6rp9"},"title":"HLA-A*02:01 presenting \"SLLMWITQV\" to Alpha/Beta T cell receptor at 3.12Å resolution","unique_chain_count":5}}