{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA34746","locus":"hla-b","match_type":"histo:exact","name":"HLA-B*07:02","slug":"hla_b_07_02","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"6avg_1","chains":["H","C","D","G","P"],"downloaded_at":"2022-11-09T14:35:37.067301"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["H","A"],"match_type":"histo:assign_chains","score":0.96,"sequence":"LSLSGLEAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["G","F"],"match_type":"histo:assign_chains","score":0.81,"sequence":"MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHDQYAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGECVEWLRRYLENGKDKLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSSQSTVPIVGIVAGLAVLAVVVIGAVVAAVMCRRKSSGGKGGSYSQAACSDSAQGSDVSLTA"},"peptide":{"chains":["Q","P"],"match_type":"histo:classify_peptide","sequence":"APRGPHGGAASGL"},"tcr_alpha":{"chains":["C"],"match_type":"stcrdab","sequence":"MLAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEVASLFIPADRKSSTLSLPRVSLSDTAVYYCLVVDQKLVFGTGTRLLVSPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS","subgroup":"TRAV4"},"tcr_beta":{"chains":["D"],"match_type":"stcrdab","sequence":"MDSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNILERFSAQQFPDLHSELNLSSLELGDSALYFCASSGGHTGSNEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD","subgroup":"TRBV9"}},"chronology":{"deposition_date":"2017-09-02","deposition_year":2017,"release_date":"2018-02-28","release_year":2018,"revision_date":"2018-03-28","revision_year":2018},"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-b","manually_edited":{},"missing_residues":[],"page_title":"6AVG | HLA-B*07:02 presenting \"APRGPHGGAASGL\" to Alpha/Beta T cell receptor","pdb_code":"6avg","pdb_title":"Crystal structure of the kfj37 TCR-ny-eso-1-hla-b*07:02 complex","peptide":{"P":{"actual_length":13,"actual_sequence":"APRGPHGGAASGL","chain_id":"P","features":["correct_sequence_and_length"],"full_length":13,"full_sequence":"APRGPHGGAASGL"},"Q":{"actual_length":13,"actual_sequence":"APRGPHGGAASGL","chain_id":"Q","features":["correct_sequence_and_length"],"full_length":13,"full_sequence":"APRGPHGGAASGL"}},"peptide_length":13,"peptide_length_name":"tridecamer","peptide_neighbours":{"1":{"neighbours":[{"position":171,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":63,"residue":"ASN"},{"position":5,"residue":"MET"},{"position":62,"residue":"ARG"},{"position":167,"residue":"TRP"},{"position":7,"residue":"TYR"}],"position":1,"residue":"ALA"},"10":{"neighbours":[{"position":73,"residue":"THR"},{"position":152,"residue":"GLU"}],"position":10,"residue":"ALA"},"11":{"neighbours":[{"position":147,"residue":"TRP"},{"position":146,"residue":"LYS"},{"position":152,"residue":"GLU"},{"position":156,"residue":"ARG"},{"position":73,"residue":"THR"}],"position":11,"residue":"SER"},"12":{"neighbours":[{"position":147,"residue":"TRP"},{"position":146,"residue":"LYS"},{"position":77,"residue":"SER"},{"position":73,"residue":"THR"}],"position":12,"residue":"GLY"},"13":{"neighbours":[{"position":123,"residue":"TYR"},{"position":95,"residue":"LEU"},{"position":80,"residue":"ASN"},{"position":147,"residue":"TRP"},{"position":84,"residue":"TYR"},{"position":81,"residue":"LEU"},{"position":146,"residue":"LYS"},{"position":77,"residue":"SER"},{"position":116,"residue":"TYR"},{"position":143,"residue":"THR"}],"position":13,"residue":"LEU"},"2":{"neighbours":[{"position":99,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":7,"residue":"TYR"},{"position":67,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":9,"residue":"TYR"},{"position":66,"residue":"ILE"},{"position":45,"residue":"GLU"},{"position":63,"residue":"ASN"}],"position":2,"residue":"PRO"},"3":{"neighbours":[{"position":66,"residue":"ILE"},{"position":99,"residue":"TYR"},{"position":155,"residue":"GLN"},{"position":116,"residue":"TYR"},{"position":114,"residue":"ASP"},{"position":156,"residue":"ARG"},{"position":70,"residue":"GLN"},{"position":62,"residue":"ARG"},{"position":159,"residue":"TYR"},{"position":9,"residue":"TYR"}],"position":3,"residue":"ARG"},"4":{"neighbours":[{"position":62,"residue":"ARG"},{"position":66,"residue":"ILE"}],"position":4,"residue":"GLY"},"5":{"neighbours":[{"position":155,"residue":"GLN"},{"position":66,"residue":"ILE"}],"position":5,"residue":"PRO"},"6":{"neighbours":[{"position":159,"residue":"TYR"},{"position":158,"residue":"ALA"},{"position":155,"residue":"GLN"},{"position":163,"residue":"GLU"}],"position":6,"residue":"HIS"}},"peptide_sequence":"APRGPHGGAASGL","pockets":{"a":{"a159":{"number":159,"one_letter":"A","three_letter":"ALA"},"a163":{"number":163,"one_letter":"A","three_letter":"ALA"},"a167":{"number":167,"one_letter":"T","three_letter":"THR"},"a171":{"number":171,"one_letter":"W","three_letter":"TRP"},"a5":{"number":5,"one_letter":"A","three_letter":"ALA"},"a59":{"number":59,"one_letter":"R","three_letter":"ARG"},"a63":{"number":63,"one_letter":"D","three_letter":"ASP"},"a66":{"number":66,"one_letter":"S","three_letter":"SER"},"a7":{"number":7,"one_letter":"R","three_letter":"ARG"}},"b":{"a24":{"number":24,"one_letter":"A","three_letter":"ALA"},"a34":{"number":34,"one_letter":"T","three_letter":"THR"},"a45":{"number":45,"one_letter":"R","three_letter":"ARG"},"a63":{"number":63,"one_letter":"D","three_letter":"ASP"},"a66":{"number":66,"one_letter":"S","three_letter":"SER"},"a67":{"number":67,"one_letter":"P","three_letter":"PRO"},"a7":{"number":7,"one_letter":"R","three_letter":"ARG"},"a70":{"number":70,"one_letter":"E","three_letter":"GLU"},"a9":{"number":9,"one_letter":"V","three_letter":"VAL"},"a99":{"number":99,"one_letter":"R","three_letter":"ARG"}},"c":{"a70":{"number":70,"one_letter":"E","three_letter":"GLU"},"a73":{"number":73,"one_letter":"A","three_letter":"ALA"},"a74":{"number":74,"one_letter":"P","three_letter":"PRO"},"a9":{"number":9,"one_letter":"V","three_letter":"VAL"},"a97":{"number":97,"one_letter":"T","three_letter":"THR"}},"d":{"a114":{"number":114,"one_letter":"A","three_letter":"ALA"},"a155":{"number":155,"one_letter":"R","three_letter":"ARG"},"a156":{"number":156,"one_letter":"S","three_letter":"SER"},"a159":{"number":159,"one_letter":"A","three_letter":"ALA"},"a160":{"number":160,"one_letter":"A","three_letter":"ALA"},"a99":{"number":99,"one_letter":"R","three_letter":"ARG"}},"e":{"a114":{"number":114,"one_letter":"A","three_letter":"ALA"},"a147":{"number":147,"one_letter":"Y","three_letter":"TYR"},"a152":{"number":152,"one_letter":"E","three_letter":"GLU"},"a156":{"number":156,"one_letter":"S","three_letter":"SER"},"a97":{"number":97,"one_letter":"T","three_letter":"THR"}},"f":{"a116":{"number":116,"one_letter":"S","three_letter":"SER"},"a123":{"number":123,"one_letter":"Y","three_letter":"TYR"},"a143":{"number":143,"one_letter":"D","three_letter":"ASP"},"a146":{"number":146,"one_letter":"D","three_letter":"ASP"},"a147":{"number":147,"one_letter":"Y","three_letter":"TYR"},"a77":{"number":77,"one_letter":"E","three_letter":"GLU"},"a80":{"number":80,"one_letter":"G","three_letter":"GLY"},"a81":{"number":81,"one_letter":"P","three_letter":"PRO"},"a84":{"number":84,"one_letter":"W","three_letter":"TRP"},"a95":{"number":95,"one_letter":"A","three_letter":"ALA"}}},"publication":{"abstract":"Human leukocyte antigen (HLA)-I molecules generally bind short peptides (8-10 amino acids), although extended HLA-I restricted peptides (>10 amino acids) can be presented to T cells. However, the function of such extended HLA-I epitopes in tumour immunity, and how they would be recognised by T-cell receptors (TCR) remains unclear. Here we show that the structures of two distinct TCRs (TRAV4+TRAJ21+-TRBV28+TRBJ2-3+ and TRAV4 + TRAJ8+-TRBV9+TRBJ2-1+), originating from a polyclonal T-cell repertoire, bind to HLA-B*07:02, presenting a 13-amino-acid-long tumour-associated peptide, NY-ESO-160-72. Comparison of the structures reveals that the two TCRs differentially binds NY-ESO-160-72-HLA-B*07:02 complex, and induces differing extent of conformational change of the NY-ESO-160-72 epitope. Accordingly, polyclonal TCR usage towards an extended HLA-I restricted tumour epitope translates to differing TCR recognition modes, whereby extensive flexibility at the TCR-pHLA-I interface engenders recognition.","bibjson":{"author":[{"initials":"KF","lastname":"Chan","name":"Chan KF"},{"initials":"BS","lastname":"Gully","name":"Gully BS"},{"initials":"S","lastname":"Gras","name":"Gras S"},{"initials":"DX","lastname":"Beringer","name":"Beringer DX"},{"initials":"L","lastname":"Kjer-Nielsen","name":"Kjer-Nielsen L"},{"initials":"J","lastname":"Cebon","name":"Cebon J"},{"initials":"J","lastname":"McCluskey","name":"McCluskey J"},{"initials":"W","lastname":"Chen","name":"Chen W"},{"initials":"J","lastname":"Rossjohn","name":"Rossjohn J"}],"identifier":[{"id":"10.1038/s41467-018-03321-w","type":"doi"},{"id":"29531227","type":"pubmed"}],"issue":["1"],"journal":{"iso_abbreviation":"Nat Commun","name":""},"pages":["1026"],"title":"Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide.","type":"article","url":"http://www.nature.com/articles/s41467-018-03321-w","volume":["9"],"year":[2018]},"in_pmc":"N","in_pmce":"Y","open_access":"Y"},"resolution":"2.60","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6avg"},"rcsb":{"url":"https://www.rcsb.org/structure/6avg"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=6avg"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":{"alpha":{"chains":["C"],"subgroup":"TRAV4"},"beta":{"chains":["D"],"subgroup":"TRBV9"},"mhc_type":"class_i","pdb_code":"6avg"},"title":"HLA-B*07:02 presenting \"APRGPHGGAASGL\" to Alpha/Beta T cell receptor at 2.60Å resolution","unique_chain_count":5}}