{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA34423","locus":"hla-b","match_type":"histo:fuzzy","name":"HLA-B*35:01","slug":"hla_b_35_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"2akr_1","chains":["A","B"],"downloaded_at":"2022-11-09T14:30:58.021143"},"2":{"assembly_name":"2akr_2","chains":["C","D","E"],"downloaded_at":"2022-11-09T14:30:58.558782"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B","D"],"match_type":"histo:assign_chains","score":1.0,"sequence":"IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM"},"cd1d":{"chains":["A","C"],"match_type":"histo:assign_chains","score":0.97,"sequence":"SEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWHHHHHH"}},"chronology":{"deposition_date":"2005-08-03","deposition_year":2005,"release_date":"2005-12-06","release_year":2005,"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":"hla-b","manually_edited":{},"missing_residues":[],"page_title":"2AKR | Non-classical MHC Class I molecule CD1d","pdb_code":"2akr","pdb_title":"Structural basis of sulfatide presentation by 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":"Sulfatide derived from the myelin stimulates a distinct population of CD1d-restricted natural killer T (NKT) cells. Cis-tetracosenoyl sulfatide is one of the immunodominant species in myelin as identified by proliferation, cytokine secretion, and CD1d tetramer staining. The crystal structure of mouse CD1d in complex with cis-tetracosenoyl sulfatide at 1.9 A resolution reveals that the longer cis-tetracosenoyl fatty acid chain fully occupies the A' pocket of the CD1d binding groove, whereas the sphingosine chain fills up the F' pocket. A precise hydrogen bond network in the center of the binding groove orients and positions the ceramide backbone for insertion of the lipid tails in their respective pockets. The 3'-sulfated galactose headgroup is highly exposed for presentation to the T cell receptor and projects up and away from the binding pocket due to its beta linkage, compared with the more intimate binding of the alpha-glactosyl ceramide headgroup to CD1d. These structure and binding data on sulfatide presentation by CD1d have important implications for the design of therapeutics that target T cells reactive for myelin glycolipids in autoimmune diseases of the central nervous system.","bibjson":{"author":[{"initials":"DM","lastname":"Zajonc","name":"Zajonc DM"},{"initials":"I","lastname":"Maricic","name":"Maricic I"},{"initials":"D","lastname":"Wu","name":"Wu D"},{"initials":"R","lastname":"Halder","name":"Halder R"},{"initials":"K","lastname":"Roy","name":"Roy K"},{"initials":"CH","lastname":"Wong","name":"Wong CH"},{"initials":"V","lastname":"Kumar","name":"Kumar V"},{"initials":"IA","lastname":"Wilson","name":"Wilson IA"}],"identifier":[{"id":"10.1084/jem.20051625","type":"doi"},{"id":"16314439","type":"pubmed"}],"issue":["11"],"journal":{"iso_abbreviation":"J. Exp. Med.","name":""},"pages":["1517-26"],"title":"Structural basis for CD1d presentation of a sulfatide derived from myelin and its implications for autoimmunity.","type":"article","url":"https://rupress.org/jem/article/202/11/1517/52649/Structural-basis-for-CD1d-presentation-of-a","volume":["202"],"year":[2005]},"in_pmc":"N","in_pmce":"Y","open_access":"Y"},"resolution":"1.90","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/2akr"},"rcsb":{"url":"https://www.rcsb.org/structure/2akr"}},"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 1.90Å resolution","unique_chain_count":2}}