{"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":"6xng_1","chains":["A","B","C","D","E","F","G"],"downloaded_at":"2022-11-09T14:35:06.783787"}},"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":"MEAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD","subgroup":"TRBV13"}},"chronology":{"deposition_date":"2020-07-02","deposition_year":2020,"release_date":"2021-11-10","release_year":2021,"revision_date":"2021-12-22","revision_year":2021},"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-a","manually_edited":{},"missing_residues":[],"page_title":"6XNG | Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor","pdb_code":"6xng","pdb_title":"Mhc-like protein complex structure","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":"Small molecules derived from symbiotic microbiota critically contribute to intestinal immune maturation and regulation<sup>1</sup>. However, little is known about the molecular mechanisms that control immune development in the host-microbiota environment. Here, using a targeted lipidomic analysis and synthetic approach, we carried out a multifaceted investigation of immunomodulatory \u03b1-galactosylceramides from the human symbiont Bacteroides fragilis (BfaGCs). The characteristic terminal branching of BfaGCs is the result of incorporation of branched-chain amino acids taken up in the host gut by B. fragilis. A B. fragilis knockout strain that cannot metabolize branched-chain amino acids showed reduced branching in BfaGCs, and mice monocolonized with this mutant strain had impaired colonic natural killer T\u00a0(NKT) cell regulation, implying structure-specific immunomodulatory activity. The sphinganine chain branching of BfaGCs is a critical determinant of NKT cell activation, which induces specific\u00a0immunomodulatory gene expression signatures and effector functions. Co-crystal structure and affinity analyses of CD1d-BfaGC-NKT cell receptor complexes confirmed the interaction of BfaGCs as CD1d-restricted ligands. We present a structural and molecular-level paradigm of immunomodulatory control by interactions of endobiotic metabolites with diet, microbiota and the immune system.","bibjson":{"author":[{"initials":"SF","lastname":"Oh","name":"Oh SF"},{"initials":"T","lastname":"Praveena","name":"Praveena T"},{"initials":"H","lastname":"Song","name":"Song H"},{"initials":"JS","lastname":"Yoo","name":"Yoo JS"},{"initials":"DJ","lastname":"Jung","name":"Jung DJ"},{"initials":"D","lastname":"Erturk-Hasdemir","name":"Erturk-Hasdemir D"},{"initials":"YS","lastname":"Hwang","name":"Hwang YS"},{"initials":"CC","lastname":"Lee","name":"Lee CC"},{"initials":"J","lastname":"Le Nours","name":"Le Nours J"},{"initials":"H","lastname":"Kim","name":"Kim H"},{"initials":"J","lastname":"Lee","name":"Lee J"},{"initials":"RS","lastname":"Blumberg","name":"Blumberg RS"},{"initials":"J","lastname":"Rossjohn","name":"Rossjohn J"},{"initials":"SB","lastname":"Park","name":"Park SB"},{"initials":"DL","lastname":"Kasper","name":"Kasper DL"}],"identifier":[{"id":"10.1038/s41586-021-04083-0","type":"doi"},{"id":"34759313","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"Nature","name":""},"pages":[null],"title":"Host immunomodulatory lipids created by symbionts from dietary amino acids.","type":"article","url":"https://www.nature.com/articles/s41586-021-04083-0","volume":[null],"year":[2021]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"2.79","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6xng"},"rcsb":{"url":"https://www.rcsb.org/structure/6xng"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=6xng"}},"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":"6xng"},"title":"Non-classical MHC Class I molecule CD1d with Natural Killer Alpha/Beta T cell receptor at 2.79&#8491; resolution","unique_chain_count":4}}