{"display":true,"structure":{"allele":{"alpha":{"identifier":"uniprot:P01901","locus":"h2-k","match_type":"histo:exact","name":"H2-Kb","slug":"h2_kb","species_stem":"H2"},"beta":{}},"assemblies":{"1":{"assembly_name":"3o8x_1","chains":["A","B","C","D","E","F"],"downloaded_at":"2022-11-09T14:36:10.061129"}},"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"},"tcr_alpha":{"chains":["C"],"match_type":"stcrdab","sequence":"MKTQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS","subgroup":"TRAV11"},"tcr_beta":{"chains":["D"],"match_type":"stcrdab","sequence":"MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTPPKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA","subgroup":"TRBV13"}},"chronology":{"deposition_date":"2010-08-03","deposition_year":2010,"release_date":"2010-09-29","release_year":2010,"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":"h2-k","manually_edited":{},"missing_residues":[],"page_title":"3O8X | Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor","pdb_code":"3o8x","pdb_title":"Recognition of glycolipid antigen by inkT cell 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":"Invariant natural killer T cells (iNKT cells) rapidly produce effector cytokines. In this study, we report the first crystal structures of the iNKT cell T cell receptor (TCR) bound to two natural, microbial glycolipids presented by CD1d. Binding of the TCR induced CDR3-\u03b1-dependent structural changes in the F' roof of CD1d; these changes resemble those occurring in the absence of TCR engagement when the highly potent synthetic antigen \u03b1-galactosylceramide (\u03b1-GalCer) binds CD1d. Furthermore, in the Borrelia burgdorferi \u03b1-galactosyl diacylglycerol-CD1d complex, TCR binding caused a marked repositioning of the galactose sugar into an orientation that closely resembles \u03b1-GalCer. The TCR-dependent reorientation of the sugar, together with the induced CD1d fit, may explain the weaker potency of the microbial antigens compared with \u03b1-GalCer. We propose that the TCR of iNKT cells binds with a conserved footprint onto CD1d, regardless of the bound glycolipid antigen, and that for microbial antigens this unique binding mode requires TCR-initiated conformational changes.","bibjson":{"author":[{"initials":"Y","lastname":"Li","name":"Li Y"},{"initials":"E","lastname":"Girardi","name":"Girardi E"},{"initials":"J","lastname":"Wang","name":"Wang J"},{"initials":"ED","lastname":"Yu","name":"Yu ED"},{"initials":"GF","lastname":"Painter","name":"Painter GF"},{"initials":"M","lastname":"Kronenberg","name":"Kronenberg M"},{"initials":"DM","lastname":"Zajonc","name":"Zajonc DM"}],"identifier":[{"id":"10.1084/jem.20101335","type":"doi"},{"id":"20921281","type":"pubmed"}],"issue":["11"],"journal":{"iso_abbreviation":"J. Exp. Med.","name":""},"pages":["2383-93"],"title":"The V\ufffd\ufffd14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode.","type":"article","url":"https://rupress.org/jem/article/207/11/2383/40656/The-V%CE%B114-invariant-natural-killer-T-cell-TCR","volume":["207"],"year":[2010]},"in_pmc":"Y","in_pmce":"Y","open_access":"Y"},"resolution":"2.74","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/3o8x"},"rcsb":{"url":"https://www.rcsb.org/structure/3o8x"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=3o8x"}},"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":"3o8x"},"title":"Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 2.74Å resolution","unique_chain_count":4}}