{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA34732","locus":"hla-a","match_type":"histo:exact","name":"HLA-A*11:01","slug":"hla_a_11_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"5gsd_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:39:14.768567"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":1.0,"sequence":"IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["A"],"match_type":"histo:assign_chains","score":0.92,"sequence":"GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE"},"peptide":{"chains":["C"],"match_type":"histo:classify_peptide","sequence":"SSCPLSK"}},"chronology":{"deposition_date":"2016-08-15","deposition_year":2016,"release_date":"2017-08-09","release_year":2017,"revision_date":"2017-09-27","revision_year":2017},"class":"class_i","classical":true,"complex_type":"class_i_with_peptide","components":["class_i_alpha","beta2m","peptide"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"hla-a","manually_edited":{},"missing_residues":[],"page_title":"5GSD | HLA-A*11:01 binding \"SSCPLSK\"","pdb_code":"5gsd","pdb_title":"Crystal structure of lmp2 peptide from ebv in complex with hla-a*11:01","peptide":{"C":{"actual_length":7,"actual_sequence":"SSCPLSK","chain_id":"C","features":["correct_sequence_and_length","short_peptide"],"full_length":7,"full_sequence":"SSCPLSK"}},"peptide_length":7,"peptide_length_name":"heptamer","peptide_neighbours":{"1":{"neighbours":[{"position":159,"residue":"TYR"},{"position":9,"residue":"TYR"},{"position":163,"residue":"ARG"},{"position":66,"residue":"ASN"},{"position":7,"residue":"TYR"},{"position":99,"residue":"TYR"},{"position":63,"residue":"GLU"},{"position":45,"residue":"MET"},{"position":67,"residue":"VAL"}],"position":1,"residue":"SER"},"2":{"neighbours":[{"position":156,"residue":"GLN"},{"position":99,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":9,"residue":"TYR"},{"position":66,"residue":"ASN"},{"position":114,"residue":"ARG"}],"position":2,"residue":"SER"},"3":{"neighbours":[{"position":156,"residue":"GLN"},{"position":155,"residue":"GLN"},{"position":70,"residue":"GLN"},{"position":66,"residue":"ASN"}],"position":3,"residue":"CYS"},"4":{"neighbours":[{"position":69,"residue":"ALA"},{"position":155,"residue":"GLN"},{"position":70,"residue":"GLN"},{"position":73,"residue":"THR"},{"position":66,"residue":"ASN"}],"position":4,"residue":"PRO"},"5":{"neighbours":[{"position":77,"residue":"ASP"},{"position":152,"residue":"ALA"},{"position":147,"residue":"TRP"},{"position":133,"residue":"TRP"},{"position":114,"residue":"ARG"},{"position":156,"residue":"GLN"},{"position":155,"residue":"GLN"},{"position":70,"residue":"GLN"},{"position":73,"residue":"THR"}],"position":5,"residue":"LEU"},"6":{"neighbours":[{"position":73,"residue":"THR"},{"position":77,"residue":"ASP"},{"position":147,"residue":"TRP"},{"position":146,"residue":"LYS"}],"position":6,"residue":"SER"},"7":{"neighbours":[{"position":114,"residue":"ARG"},{"position":143,"residue":"THR"},{"position":146,"residue":"LYS"},{"position":123,"residue":"TYR"},{"position":116,"residue":"ASP"},{"position":97,"residue":"ILE"},{"position":95,"residue":"ILE"},{"position":80,"residue":"THR"},{"position":84,"residue":"TYR"},{"position":81,"residue":"LEU"},{"position":77,"residue":"ASP"},{"position":124,"residue":"ILE"},{"position":147,"residue":"TRP"}],"position":7,"residue":"LYS"}},"peptide_sequence":"SSCPLSK","pockets":{"a":{"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a163":{"number":163,"one_letter":"R","three_letter":"ARG"},"a167":{"number":167,"one_letter":"W","three_letter":"TRP"},"a171":{"number":171,"one_letter":"Y","three_letter":"TYR"},"a5":{"number":5,"one_letter":"M","three_letter":"MET"},"a59":{"number":59,"one_letter":"Y","three_letter":"TYR"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"N","three_letter":"ASN"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"A","three_letter":"ALA"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"M","three_letter":"MET"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"N","three_letter":"ASN"},"a67":{"number":67,"one_letter":"V","three_letter":"VAL"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"Q","three_letter":"GLN"},"a9":{"number":9,"one_letter":"Y","three_letter":"TYR"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"Q","three_letter":"GLN"},"a73":{"number":73,"one_letter":"T","three_letter":"THR"},"a74":{"number":74,"one_letter":"D","three_letter":"ASP"},"a9":{"number":9,"one_letter":"Y","three_letter":"TYR"},"a97":{"number":97,"one_letter":"I","three_letter":"ILE"}},"d":{"a114":{"number":114,"one_letter":"R","three_letter":"ARG"},"a155":{"number":155,"one_letter":"Q","three_letter":"GLN"},"a156":{"number":156,"one_letter":"Q","three_letter":"GLN"},"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a160":{"number":160,"one_letter":"L","three_letter":"LEU"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"e":{"a114":{"number":114,"one_letter":"R","three_letter":"ARG"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"A","three_letter":"ALA"},"a156":{"number":156,"one_letter":"Q","three_letter":"GLN"},"a97":{"number":97,"one_letter":"I","three_letter":"ILE"}},"f":{"a116":{"number":116,"one_letter":"D","three_letter":"ASP"},"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":"I","three_letter":"ILE"}}},"publication":{"abstract":"Host CD8 T cell response to viral infections involves recognition of 8-10-mer peptides presented by MHC-I molecules. However, proteasomes generate predominantly 2-7-mer peptides, but the role of these peptides is largely unknown. Here, we show that single short peptides of <8-mer from Latent Membrane Protein 2 (LMP2) of Epstein Barr Virus (EBV) can bind HLA-A*11:01 and stimulate CD8<sup>+</sup> cells. Surprisingly, two peptide fragments between 4-7-mer derived from LMP2<sub>(340-349)</sub> were able to complement each other, forming combination epitopes that can stimulate specific CD8<sup>+</sup> T cell responses. Moreover, peptides from self-antigens can complement non-self peptides within the HLA binding cleft, forming neoepitopes. Solved structures of a tetra-complex comprising two peptides, HLA and \u03b22-microglobulin revealed the free terminals of the two peptides to adopt an upward conformation directed towards the T cell receptor. Our results demonstrate a previously unknown mix-and-match combination of dual peptide occupancy in HLA that can generate vast combinatorial complexity.","bibjson":{"author":[{"initials":"Z","lastname":"Xiao","name":"Xiao Z"},{"initials":"Z","lastname":"Ye","name":"Ye Z"},{"initials":"VS","lastname":"Tadwal","name":"Tadwal VS"},{"initials":"M","lastname":"Shen","name":"Shen M"},{"initials":"EC","lastname":"Ren","name":"Ren EC"}],"identifier":[{"id":"10.1038/s41598-017-05171-w","type":"doi"},{"id":"28698575","type":"pubmed"}],"issue":["1"],"journal":{"iso_abbreviation":"Sci Rep","name":""},"pages":["5072"],"title":"Dual non-contiguous peptide occupancy of HLA class I evoke antiviral human CD8 T cell response and form neo-epitopes with self-antigens.","type":"article","url":"http://www.nature.com/articles/s41598-017-05171-w","volume":["7"],"year":[2017]},"in_pmc":"N","in_pmce":"Y","open_access":"Y"},"resolution":"2.30","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/5gsd"},"rcsb":{"url":"https://www.rcsb.org/structure/5gsd"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-A*11:01 binding \"SSCPLSK\" at 2.30&#8491; resolution","unique_chain_count":3}}