{"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":"4zak_1","chains":["A","B","C","D","E"],"downloaded_at":"2022-11-09T14:33:55.709027"}},"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":"2015-04-13","deposition_year":2015,"release_date":"2015-07-01","release_year":2015,"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":"4ZAK | Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor","pdb_code":"4zak","pdb_title":"Crystal structure of the mCD1d/db06-1/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":"In this article, we characterize a novel Ag for invariant NKT (iNKT) cells capable of producing an especially robust Th1 response. This glycosphingolipid, DB06-1, is similar in chemical structure to the well-studied \u03b1-galactosylceramide (\u03b1GalCer), with the only change being a single atom: the substitution of a carbonyl oxygen with a sulfur atom. Although DB06-1 is not a more effective Ag in vitro, the small chemical change has a marked impact on the ability of this lipid Ag to stimulate iNKT cells in vivo, with increased IFN-\u03b3 production at 24 h compared with \u03b1GalCer, increased IL-12, and increased activation of NK cells to produce IFN-\u03b3. These changes are correlated with an enhanced ability of DB06-1 to load in the CD1d molecules expressed by dendritic cells in vivo. Moreover, structural studies suggest a tighter fit into the CD1d binding groove by DB06-1 compared with \u03b1GalCer. Surprisingly, when iNKT cells previously exposed to DB06-1 are restimulated weeks later, they have greatly increased IL-10 production. Therefore, our data are consistent with a model whereby augmented and or prolonged presentation of a glycolipid Ag leads to increased activation of NK cells and a Th1-skewed immune response, which may result, in part, from enhanced loading into CD1d. Furthermore, our data suggest that strong antigenic stimulation in vivo may lead to the expansion of IL-10-producing iNKT cells, which could counteract the benefits of increased early IFN-\u03b3 production.","bibjson":{"author":[{"initials":"AM","lastname":"Birkholz","name":"Birkholz AM"},{"initials":"E","lastname":"Girardi","name":"Girardi E"},{"initials":"G","lastname":"Wingender","name":"Wingender G"},{"initials":"A","lastname":"Khurana","name":"Khurana A"},{"initials":"J","lastname":"Wang","name":"Wang J"},{"initials":"M","lastname":"Zhao","name":"Zhao M"},{"initials":"S","lastname":"Zahner","name":"Zahner S"},{"initials":"PA","lastname":"Illarionov","name":"Illarionov PA"},{"initials":"X","lastname":"Wen","name":"Wen X"},{"initials":"M","lastname":"Li","name":"Li M"},{"initials":"W","lastname":"Yuan","name":"Yuan W"},{"initials":"SA","lastname":"Porcelli","name":"Porcelli SA"},{"initials":"GS","lastname":"Besra","name":"Besra GS"},{"initials":"DM","lastname":"Zajonc","name":"Zajonc DM"},{"initials":"M","lastname":"Kronenberg","name":"Kronenberg M"}],"identifier":[{"id":"10.4049/jimmunol.1500070","type":"doi"},{"id":"26078271","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"J. Immunol.","name":""},"pages":[null],"title":"A Novel Glycolipid Antigen for NKT Cells That Preferentially Induces IFN-\ufffd\ufffd Production.","type":"article","url":"http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1500070","volume":[null],"year":[2015]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"2.82","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/4zak"},"rcsb":{"url":"https://www.rcsb.org/structure/4zak"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=4zak"}},"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":"4zak"},"title":"Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 2.82Å resolution","unique_chain_count":4}}