{"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":"4y16_1","chains":["A","B","C","D","E","F"],"downloaded_at":"2022-11-09T14:40:55.118473"}},"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":0.97,"sequence":"SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH"},"chimeric_tcr_alpha":{"chains":["C"],"match_type":"histo:override","sequence":"MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS"},"chimeric_tcr_beta":{"chains":["D"],"match_type":"histo:override","sequence":"MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTPPKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA"},"note":"not yet in STCRdab"},"chronology":{"deposition_date":"2015-02-06","deposition_year":2015,"release_date":"2015-06-03","release_year":2015,"revision_date":"2020-07-29","revision_year":2020},"class":"class_i","classical":false,"complex_type":"cd1d_with_chimeric_alpha_beta_tcr","components":["cd1d","beta2m","chimeric_tcr_alpha","chimeric_tcr_beta"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"hla-a","manually_edited":{},"missing_residues":[],"page_title":"4Y16 | Non-classical MHC Class I molecule CD1d with chimeric Alpha/Beta T cell receptor","pdb_code":"4y16","pdb_title":"Crystal structure of the mCD1d/nc-agc/inkTCR ternary complex","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 ability of different glycosphingolipids (GSLs) to activate type I natural killer T cells (NKT cells) has been known for 2 decades. The possible therapeutic use of these GSLs has been studied in many ways; however, studies are needed in which the efficacy of promising GSLs is compared under identical conditions. Here, we compare five unique GSLs structurally derived from \u03b1-galactosylceramide. We employed biophysical and biological assays, as well as x-ray crystallography to study the impact of the chemical modifications of the antigen on type I NKT cell activation. Although all glycolipids are bound by the T cell receptor of type I NKT cells in real time binding assays with high affinity, only a few activate type I NKT cells in in vivo or in vitro experiments. The differences in biological responses are likely a result of different pharmacokinetic properties of each lipid, which carry modifications at different parts of the molecule. Our results indicate a need to perform a variety of assays to ascertain the therapeutic potential of type I NKT cell GSL activators.","bibjson":{"author":[{"initials":"A","lastname":"Birkholz","name":"Birkholz A"},{"initials":"M","lastname":"Nem\ufffd\ufffdovi\ufffd\ufffd","name":"Nem\ufffd\ufffdovi\ufffd\ufffd M"},{"initials":"ED","lastname":"Yu","name":"Yu ED"},{"initials":"E","lastname":"Girardi","name":"Girardi E"},{"initials":"J","lastname":"Wang","name":"Wang J"},{"initials":"A","lastname":"Khurana","name":"Khurana A"},{"initials":"N","lastname":"Pauwels","name":"Pauwels N"},{"initials":"E","lastname":"Farber","name":"Farber E"},{"initials":"S","lastname":"Chitale","name":"Chitale S"},{"initials":"RW","lastname":"Franck","name":"Franck RW"},{"initials":"M","lastname":"Tsuji","name":"Tsuji M"},{"initials":"A","lastname":"Howell","name":"Howell A"},{"initials":"S","lastname":"Van Calenbergh","name":"Van Calenbergh S"},{"initials":"M","lastname":"Kronenberg","name":"Kronenberg M"},{"initials":"DM","lastname":"Zajonc","name":"Zajonc DM"}],"identifier":[{"id":"10.1074/jbc.m115.654814","type":"doi"},{"id":"26018083","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"J. Biol. Chem.","name":""},"pages":[null],"title":"Lipid and carbohydrate modifications of \ufffd\ufffd-galactosylceramide differently influence mouse and human type I natural killer T cell activation.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S0021925820353278","volume":[null],"year":[2015]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"2.60","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/4y16"},"rcsb":{"url":"https://www.rcsb.org/structure/4y16"}},"species":{"common_name":"Mouse","match_type":"histo:assign_species","scientific_name":"Mus musculus","slug":"mus_musculus"},"tcr":null,"title":"Non-classical MHC Class I molecule CD1d with chimeric Alpha/Beta T cell receptor at 2.60Å resolution","unique_chain_count":4}}