{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA34811","locus":"hla-b","match_type":"histo:exact","name":"HLA-B*27:05","slug":"hla_b_27_05","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"3he6_1","chains":["A","B","C","D","E"],"downloaded_at":"2022-11-09T14:37:52.518723"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":1.0,"sequence":"IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM"},"cd1d":{"chains":["A"],"match_type":"histo:assign_chains","score":1.0,"sequence":"SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSLHHILDAQKMVWNHRHHHHHH"},"tcr_alpha":{"chains":["C"],"match_type":"stcrdab","sequence":"TQVEQSPQSLVVRQGENSVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS","subgroup":"TRAV11"},"tcr_beta":{"chains":["D"],"match_type":"stcrdab","sequence":"EAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDAGGNYAEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD","subgroup":"TRBV13"}},"chronology":{"deposition_date":"2009-05-07","deposition_year":2009,"release_date":"2009-07-28","release_year":2009,"revision_date":"2020-07-29","revision_year":2020},"class":"class_i","classical":false,"complex_type":"cd1d_with_nkt_alpha_beta_tcr","components":["cd1d","beta2m","tcr_alpha","tcr_beta"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"hla-b","manually_edited":{},"missing_residues":[],"page_title":"3HE6 | Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor","pdb_code":"3he6","pdb_title":"Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse valpha14-vbeta8.2 nkt TCR","peptide":{"actual_sequence":null,"epitope_info":{},"features":[],"full_sequence":null,"gap_info":{},"gapped_sequence":null,"length":{"numeric":null,"text":null},"unnatural_amino_acids":[]},"publication":{"abstract":"The semi-invariant natural killer T cell receptor (NKT TCR) recognizes CD1d-lipid antigens. Although the TCR alpha chain is typically invariant, the beta chain expression is more diverse, where three V beta chains are commonly expressed in mice. We report the structures of V alpha 14-V beta 8.2 and V alpha 14-V beta 7 NKT TCRs in complex with CD1d-alpha-galactosylceramide (alpha-GalCer) and the 2.5 A structure of the human NKT TCR-CD1d-alpha-GalCer complex. Both V beta 8.2 and V beta 7 NKT TCRs and the human NKT TCR ligated CD1d-alpha-GalCer in a similar manner, highlighting the evolutionarily conserved interaction. However, differences within the V beta domains of the V beta 8.2 and V beta 7 NKT TCR-CD1d complexes resulted in altered TCR beta-CD1d-mediated contacts and modulated recognition mediated by the invariant alpha chain. Mutagenesis studies revealed the differing contributions of V beta 8.2 and V beta 7 residues within the CDR2 beta loop in mediating contacts with CD1d. Collectively we provide a structural basis for the differential NKT TCR V beta usage in NKT cells.","bibjson":{"author":[{"initials":"DG","lastname":"Pellicci","name":"Pellicci DG"},{"initials":"O","lastname":"Patel","name":"Patel O"},{"initials":"L","lastname":"Kjer-Nielsen","name":"Kjer-Nielsen L"},{"initials":"SS","lastname":"Pang","name":"Pang SS"},{"initials":"LC","lastname":"Sullivan","name":"Sullivan LC"},{"initials":"K","lastname":"Kyparissoudis","name":"Kyparissoudis K"},{"initials":"AG","lastname":"Brooks","name":"Brooks AG"},{"initials":"HH","lastname":"Reid","name":"Reid HH"},{"initials":"S","lastname":"Gras","name":"Gras S"},{"initials":"IS","lastname":"Lucet","name":"Lucet IS"},{"initials":"R","lastname":"Koh","name":"Koh R"},{"initials":"MJ","lastname":"Smyth","name":"Smyth MJ"},{"initials":"T","lastname":"Mallevaey","name":"Mallevaey T"},{"initials":"JL","lastname":"Matsuda","name":"Matsuda JL"},{"initials":"L","lastname":"Gapin","name":"Gapin L"},{"initials":"J","lastname":"McCluskey","name":"McCluskey J"},{"initials":"DI","lastname":"Godfrey","name":"Godfrey DI"},{"initials":"J","lastname":"Rossjohn","name":"Rossjohn J"}],"identifier":[{"id":"10.1016/j.immuni.2009.04.018","type":"doi"},{"id":"19592275","type":"pubmed"}],"issue":["1"],"journal":{"iso_abbreviation":"Immunity","name":""},"pages":["47-59"],"title":"Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S107476130900274X","volume":["31"],"year":[2009]},"in_pmc":"Y","in_pmce":"Y","open_access":"N"},"resolution":"2.90","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/3he6"},"rcsb":{"url":"https://www.rcsb.org/structure/3he6"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=3he6"}},"species":{"common_name":"Mouse","match_type":"histo:assign_species","scientific_name":"Mus musculus","slug":"mus_musculus"},"tcr":{"alpha":{"chains":["C"],"subgroup":"TRAV11"},"beta":{"chains":["D"],"subgroup":"TRBV13"},"pdb_code":"3he6"},"title":"Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 2.90Å resolution","unique_chain_count":4}}