{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-mhc:NHP10490","locus":"mamu-b","match_type":"histo:fuzzy","name":"Mamu-B*051:02","slug":"mamu_b_051_02","species_stem":"Mamu"},"beta":{}},"assemblies":{"1":{"assembly_name":"6lt6_1","chains":["A","B"],"downloaded_at":"2022-11-09T14:31:23.605463"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":0.9,"sequence":"AIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM"},"class_i_alpha":{"chains":["A"],"match_type":"histo:assign_chains","score":0.86,"sequence":"GSHSLRYFGTAVSRPGRGEPRFIYVGYVDDTQFVRFDSDAASPRTEPRAPWVEQEGPEYWEEETRRAKARAQTDRADLRTLRGYYNQSEAGSHTLQWMAGCDLGPNGRLLRGYHQSAYDGKDYIALNEDLRSWIAADMAAQNTQRKWEATRYAERFRAYLEGPCLEWLRRYLENGKETLQHADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDIEFVETRPAGDGTFQKWGAVVVPSGEEQRYTCHVQHKGLPEPLTLRWEP"}},"chronology":{"deposition_date":"2020-01-21","deposition_year":2020,"release_date":"2020-04-22","release_year":2020,"revision_date":"2020-05-27","revision_year":2020},"class":"class_i","classical":true,"complex_type":"class_i_possibly_without_peptide","components":["class_i_alpha","beta2m"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"mamu-b","manually_edited":{},"missing_residues":[],"page_title":"6LT6 | Mamu-B*051:02 possibly without \"peptide\"","pdb_code":"6lt6","pdb_title":"Crystal structure of rhesus macaque MHC Class I molecule mamu-b*05104 complexed with lysophosphatidylcholine","peptide":{"actual_sequence":null,"epitope_info":{},"features":[],"full_sequence":null,"gap_info":{},"gapped_sequence":null,"length":{"numeric":null,"text":null},"unnatural_amino_acids":[]},"pockets":{"a":{"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a163":{"number":163,"one_letter":"P","three_letter":"PRO"},"a167":{"number":167,"one_letter":"W","three_letter":"TRP"},"a171":{"number":171,"one_letter":"Y","three_letter":"TYR"},"a5":{"number":5,"one_letter":"L","three_letter":"LEU"},"a59":{"number":59,"one_letter":"Y","three_letter":"TYR"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"R","three_letter":"ARG"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"Y","three_letter":"TYR"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"T","three_letter":"THR"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"R","three_letter":"ARG"},"a67":{"number":67,"one_letter":"A","three_letter":"ALA"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"R","three_letter":"ARG"},"a9":{"number":9,"one_letter":"G","three_letter":"GLY"},"a99":{"number":99,"one_letter":"A","three_letter":"ALA"}},"c":{"a70":{"number":70,"one_letter":"R","three_letter":"ARG"},"a73":{"number":73,"one_letter":"T","three_letter":"THR"},"a74":{"number":74,"one_letter":"D","three_letter":"ASP"},"a9":{"number":9,"one_letter":"G","three_letter":"GLY"},"a97":{"number":97,"one_letter":"W","three_letter":"TRP"}},"d":{"a114":{"number":114,"one_letter":"H","three_letter":"HIS"},"a155":{"number":155,"one_letter":"R","three_letter":"ARG"},"a156":{"number":156,"one_letter":"F","three_letter":"PHE"},"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a160":{"number":160,"one_letter":"L","three_letter":"LEU"},"a99":{"number":99,"one_letter":"A","three_letter":"ALA"}},"e":{"a114":{"number":114,"one_letter":"H","three_letter":"HIS"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"Y","three_letter":"TYR"},"a156":{"number":156,"one_letter":"F","three_letter":"PHE"},"a97":{"number":97,"one_letter":"W","three_letter":"TRP"}},"f":{"a116":{"number":116,"one_letter":"S","three_letter":"SER"},"a123":{"number":123,"one_letter":"Y","three_letter":"TYR"},"a143":{"number":143,"one_letter":"T","three_letter":"THR"},"a146":{"number":146,"one_letter":"K","three_letter":"LYS"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a77":{"number":77,"one_letter":"D","three_letter":"ASP"},"a80":{"number":80,"one_letter":"T","three_letter":"THR"},"a81":{"number":81,"one_letter":"L","three_letter":"LEU"},"a84":{"number":84,"one_letter":"Y","three_letter":"TYR"},"a95":{"number":95,"one_letter":"L","three_letter":"LEU"}}},"publication":{"abstract":"Newly synthesized major histocompatibility complex (MHC) class I proteins are stabilized in the endoplasmic reticulum (ER) by binding 8-10-mer-long self-peptide antigens that are provided by transporter associated with antigen processing (TAP). These MHC class I:peptide complexes then exit the ER and reach the plasma membrane, serving to sustain the steady-state MHC class I expression on the cell surface. A novel subset of MHC class I molecules that preferentially bind lipid-containing ligands rather than conventional peptides was recently identified. The primate classical MHC class I allomorphs, Mamu-B*098 and Mamu-B*05104, are capable of binding the <i>N</i>-myristoylated 5-mer (C14-Gly-Gly-Ala-Ile-Ser) or 4-mer (C14-Gly-Gly-Ala-Ile) lipopeptides derived from the <i>N</i>-myristoylated SIV Nef protein, respectively, and of activating lipopeptide antigen-specific cytotoxic T lymphocytes. We herein demonstrate that Mamu-B*098 samples lysophosphatidylethanolamine and lysophosphatidylcholine containing up to a C20 fatty acid in the ER. The X-ray crystal structures of Mamu-B*098 and Mamu-B*05104 complexed with lysophospholipids at high resolution revealed that the B and D pockets in the antigen-binding grooves of these MHC class I molecules accommodate these lipids through a monoacylglycerol moiety. Consistent with the capacity to bind cellular lipid ligands, these two MHC class I molecules did not require TAP function for cell-surface expression. Collectively, these results indicate that peptide- and lipopeptide-presenting MHC class I subsets use distinct sources of endogenous ligands.","bibjson":{"author":[{"initials":"Y","lastname":"Shima","name":"Shima Y"},{"initials":"D","lastname":"Morita","name":"Morita D"},{"initials":"T","lastname":"Mizutani","name":"Mizutani T"},{"initials":"N","lastname":"Mori","name":"Mori N"},{"initials":"B","lastname":"Mikami","name":"Mikami B"},{"initials":"M","lastname":"Sugita","name":"Sugita M"}],"identifier":[{"id":"10.1074/jbc.RA119.011932","type":"doi"},{"id":"32269076","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"J. Biol. Chem.","name":""},"pages":[null],"title":"Crystal structures of lysophospholipid-bound MHC class I molecules.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S0021925817482019","volume":[null],"year":[2020]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"2.15","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6lt6"},"rcsb":{"url":"https://www.rcsb.org/structure/6lt6"}},"species":{"common_name":"rhesus monkey","match_type":"histo:assign_species","scientific_name":"Macaca mulatta","slug":"macaca_mulatta"},"tcr":null,"title":"Mamu-B*051:02 possibly without \"peptide\" at 2.15&#8491; resolution","unique_chain_count":2}}