{"display":true,"structure":{"allele":{"alpha":{"identifier":"uniprot:P01900","locus":"h2-d","match_type":"histo:fuzzy","name":"H2-Dd","slug":"h2_dd","species_stem":"H2"},"beta":{}},"assemblies":{"1":{"assembly_name":"2fik_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:27:09.273053"}},"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":"2005-12-29","deposition_year":2005,"release_date":"2006-03-21","release_year":2006,"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":"h2-d","manually_edited":{},"missing_residues":[],"page_title":"2FIK | Non-classical MHC Class I molecule CD1d","pdb_code":"2fik","pdb_title":"Structure of a microbial glycosphingolipid bound to mouse CD1d","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 provide an innate-type immune response upon T cell receptor interaction with CD1d-presented antigens. We demonstrate through equilibrium tetramer binding and antigen presentation assays with Valpha14i-positive NKT cell hybridomas that the Sphingomonas glycolipid alpha-galacturonosyl ceramide (GalA-GSL) is a NKT cell agonist that is significantly weaker than alpha-galactosylceramide (alpha-GalCer), the most potent known NKT agonist. For GalA-GSL, a shorter fatty acyl chain, an absence of the 4-OH on the sphingosine tail and a 6'-COOH group on the galactose moiety account for its observed antigenic potency. We further determined the crystal structure of mCD1d in complex with GalA-GSL at 1.8-A resolution. The overall binding mode of GalA-GSL to mCD1d is similar to that of the short-chain alpha-GalCer ligand PBS-25, but its sphinganine chain is more deeply inserted into the F' pocket due to alternate hydrogen-bonding interactions between the sphinganine 3-OH with Asp-80. Subsequently, a slight lateral shift (>1 A) of the galacturonosyl head group is noted at the CD1 surface compared with the galactose of alpha-GalCer. Because the relatively short C(14) fatty acid of GalA-GSL does not fully occupy the A' pocket, a spacer lipid is found that stabilizes this pocket. The lipid spacer was identified by GC/MS as a mixture of saturated and monounsaturated palmitic acid (C(16)). Comparison of available crystal structures of alpha-anomeric glycosphingolipids now sheds light on the structural basis of their differential antigenic potency and has led to the design and synthesis of NKT cell agonists with enhanced cell-based stimulatory activities compared with alpha-GalCer.","bibjson":{"author":[{"initials":"D","lastname":"Wu","name":"Wu D"},{"initials":"DM","lastname":"Zajonc","name":"Zajonc DM"},{"initials":"M","lastname":"Fujio","name":"Fujio M"},{"initials":"BA","lastname":"Sullivan","name":"Sullivan BA"},{"initials":"Y","lastname":"Kinjo","name":"Kinjo Y"},{"initials":"M","lastname":"Kronenberg","name":"Kronenberg M"},{"initials":"IA","lastname":"Wilson","name":"Wilson IA"},{"initials":"CH","lastname":"Wong","name":"Wong CH"}],"identifier":[{"id":"10.1073/pnas.0600285103","type":"doi"},{"id":"16537470","type":"pubmed"}],"issue":["11"],"journal":{"iso_abbreviation":"Proc. Natl. Acad. Sci. U.S.A.","name":""},"pages":["3972-7"],"title":"Design of natural killer T cell activators: structure and function of a microbial glycosphingolipid bound to mouse CD1d.","type":"article","url":"https://pnas.org/doi/full/10.1073/pnas.0600285103","volume":["103"],"year":[2006]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"1.80","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/2fik"},"rcsb":{"url":"https://www.rcsb.org/structure/2fik"}},"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 1.80Å resolution","unique_chain_count":2}}