{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-mhc:CHICKEN08580","locus":"gaga-bf2","match_type":"histo:fuzzy","name":"Gaga-BF2*021:01","slug":"gaga_bf2_021_01","species_stem":"Gaga"},"beta":{}},"assemblies":{"1":{"assembly_name":"3gmo_1","chains":["A","B","C","D"],"downloaded_at":"2022-11-09T14:45:03.553820"}},"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":"SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWGSHHHHHH"}},"chronology":{"deposition_date":"2009-03-14","deposition_year":2009,"release_date":"2009-11-10","release_year":2009,"revision_date":"2020-07-29","revision_year":2020},"class":"class_i","classical":false,"complex_type":"cd1d","components":["cd1d","beta2m"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"gaga-bf2","manually_edited":{},"missing_residues":[],"page_title":"3GMO | Non-classical MHC Class I molecule CD1d","pdb_code":"3gmo","pdb_title":"Structure of mouse CD1d in complex with c8phf","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":"Natural killer T (NKT) cells are a subset of T cells that are activated by CD1d-glycolipid complexes through a semi-invariant alphabeta T cell receptor (NKT TCR). Upon activation, NKT cells secrete regulatory cytokines that are implicated in T helper cell responses. alpha-Galactosylceramide (alpha-GalCer) is a potent NKT cell agonist when presented by CD1d. Phenyl ring substitutions of the alpha-GalCer fatty acid moiety were recently found to be superior in eliciting regulatory cytokines. Crystal structures of four new mouse CD1d-lipid complexes (five structures), a new PBS-25 complex, and CD1d with an endogenous ligand, at 1.6-1.9 A resolution, reveal that the alpha-GalCer phenyl analogues impart minor structural differences to the A'-pocket, while the sphingosine and galactose moieties, important for NKT TCR recognition, remain virtually unchanged. The observed differences in cytokine-release profiles appear to be associated with increased stability of the CD1d-glycolipid complexes rather than increased affinity for the NKT TCR. Furthermore, comparison of mouse CD1d-glycolipid complexes in different crystallographic space groups reveals considerable conformational variation, particularly above the F'-pocket, the primary site of interaction with the NKT TCR. We propose that modifications of the sphingosine moiety or other substitutions that decrease alpha-GalCer flexibility would stabilize the F'-pocket. Such compounds might then increase CD1d affinity for the NKT TCR and further enhance the stimulatory and regulatory properties of alpha-GalCer derivatives.","bibjson":{"author":[{"initials":"A","lastname":"Schiefner","name":"Schiefner A"},{"initials":"M","lastname":"Fujio","name":"Fujio M"},{"initials":"D","lastname":"Wu","name":"Wu D"},{"initials":"CH","lastname":"Wong","name":"Wong CH"},{"initials":"IA","lastname":"Wilson","name":"Wilson IA"}],"identifier":[{"id":"10.1016/j.jmb.2009.08.061","type":"doi"},{"id":"19732779","type":"pubmed"}],"issue":["1"],"journal":{"iso_abbreviation":"J. Mol. Biol.","name":""},"pages":["71-82"],"title":"Structural evaluation of potent NKT cell agonists: implications for design of novel stimulatory ligands.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S002228360901081X","volume":["394"],"year":[2009]},"in_pmc":"Y","in_pmce":"Y","open_access":"N"},"resolution":"1.60","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/3gmo"},"rcsb":{"url":"https://www.rcsb.org/structure/3gmo"}},"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 at 1.60Å resolution","unique_chain_count":2}}