{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA35266","locus":"hla-a","match_type":"histo:exact","name":"HLA-A*02:01","slug":"hla_a_02_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"4wj5_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:33:47.604806"},"2":{"assembly_name":"4wj5_2","chains":["D","E","F"],"downloaded_at":"2022-11-09T14:33:48.065057"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B","E"],"match_type":"histo:assign_chains","score":0.99,"sequence":"MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["A","D"],"match_type":"histo:assign_chains","score":1.0,"sequence":"GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE"},"peptide":{"chains":["C","F"],"match_type":"histo:classify_peptide","sequence":"XVAGIGILTX"}},"chronology":{"deposition_date":"2014-09-29","deposition_year":2014,"release_date":"2014-10-29","release_year":2014,"revision_date":"2014-11-19","revision_year":2014},"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":"4WJ5 | HLA-A*02:01 binding \"XVAGIGILTX\"","pdb_code":"4wj5","pdb_title":"Structure of hla-a2 in complex with an altered peptide ligands based on mart-1 variant epitope","peptide":{"C":{"actual_length":8,"actual_sequence":"XAGIGILT","chain_id":"C","features":["contains_unnatural","central_gap"],"full_length":10,"full_sequence":"XVAGIGILTX","gapped_sequence":"XAGIGILT"},"F":{"actual_length":8,"actual_sequence":"XAGIGILT","chain_id":"F","features":["contains_unnatural","central_gap"],"full_length":10,"full_sequence":"XVAGIGILTX","gapped_sequence":"XAGIGILT"}},"peptide_length":10,"peptide_length_name":"decamer","peptide_neighbours":{"2":{"neighbours":[{"position":70,"residue":"HIS"},{"position":159,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":99,"residue":"TYR"}],"position":2,"residue":"ALA"},"3":{"neighbours":[{"position":159,"residue":"TYR"},{"position":66,"residue":"LYS"}],"position":3,"residue":"GLY"},"4":{"neighbours":[{"position":159,"residue":"TYR"},{"position":158,"residue":"ALA"},{"position":155,"residue":"GLN"},{"position":156,"residue":"LEU"}],"position":4,"residue":"ILE"},"5":{"neighbours":[{"position":114,"residue":"HIS"},{"position":152,"residue":"VAL"},{"position":155,"residue":"GLN"},{"position":156,"residue":"LEU"},{"position":97,"residue":"ARG"}],"position":5,"residue":"GLY"},"6":{"neighbours":[{"position":114,"residue":"HIS"},{"position":70,"residue":"HIS"},{"position":74,"residue":"HIS"},{"position":156,"residue":"LEU"},{"position":97,"residue":"ARG"},{"position":73,"residue":"THR"},{"position":99,"residue":"TYR"}],"position":6,"residue":"ILE"},"7":{"neighbours":[{"position":150,"residue":"ALA"},{"position":146,"residue":"LYS"},{"position":152,"residue":"VAL"},{"position":147,"residue":"TRP"},{"position":97,"residue":"ARG"},{"position":73,"residue":"THR"},{"position":77,"residue":"ASP"}],"position":7,"residue":"LEU"},"8":{"neighbours":[{"position":146,"residue":"LYS"},{"position":147,"residue":"TRP"},{"position":73,"residue":"THR"},{"position":76,"residue":"VAL"},{"position":77,"residue":"ASP"}],"position":8,"residue":"THR"}},"peptide_sequence":"XVAGIGILTX","pockets":{"a":{"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a163":{"number":163,"one_letter":"T","three_letter":"THR"},"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":"K","three_letter":"LYS"},"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":"K","three_letter":"LYS"},"a67":{"number":67,"one_letter":"V","three_letter":"VAL"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"H","three_letter":"HIS"},"a9":{"number":9,"one_letter":"F","three_letter":"PHE"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"H","three_letter":"HIS"},"a73":{"number":73,"one_letter":"T","three_letter":"THR"},"a74":{"number":74,"one_letter":"H","three_letter":"HIS"},"a9":{"number":9,"one_letter":"F","three_letter":"PHE"},"a97":{"number":97,"one_letter":"R","three_letter":"ARG"}},"d":{"a114":{"number":114,"one_letter":"H","three_letter":"HIS"},"a155":{"number":155,"one_letter":"Q","three_letter":"GLN"},"a156":{"number":156,"one_letter":"L","three_letter":"LEU"},"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":"H","three_letter":"HIS"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"V","three_letter":"VAL"},"a156":{"number":156,"one_letter":"L","three_letter":"LEU"},"a97":{"number":97,"one_letter":"R","three_letter":"ARG"}},"f":{"a116":{"number":116,"one_letter":"Y","three_letter":"TYR"},"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":"V","three_letter":"VAL"}}},"publication":{"abstract":"Virus or tumor Ag-derived peptides that are displayed by MHC class I molecules are attractive starting points for vaccine development because they induce strong protective and therapeutic cytotoxic T cell responses. In thus study, we show that the MHC binding and consequent T cell reactivity against several HLA-A*02 restricted epitopes can be further improved through the incorporation of nonproteogenic amino acids at primary and secondary anchor positions. We screened more than 90 nonproteogenic, synthetic amino acids through a range of epitopes and tested more than 3000 chemically enhanced altered peptide ligands (CPLs) for binding affinity to HLA-A*0201. With this approach, we designed CPLs of viral epitopes, of melanoma-associated Ags, and of the minor histocompatibility Ag UTA2-1, which is currently being evaluated for its antileukemic activity in clinical dendritic cell vaccination trials. The crystal structure of one of the CPLs in complex with HLA-A*0201 revealed the molecular interactions likely responsible for improved binding. The best CPLs displayed enhanced affinity for MHC, increasing MHC stability and prolonging recognition by Ag-specific T cells and, most importantly, they induced accelerated expansion of antitumor T cell frequencies in vitro and in vivo as compared with the native epitope. Eventually, we were able to construct a toolbox of preferred nonproteogenic residues with which practically any given HLA-A*02 restricted epitope can be readily optimized. These CPLs could improve the therapeutic outcome of vaccination strategies or can be used for ex vivo enrichment and faster expansion of Ag-specific T cells for transfer into patients.","bibjson":{"author":[{"initials":"R","lastname":"Hoppes","name":"Hoppes R"},{"initials":"R","lastname":"Oostvogels","name":"Oostvogels R"},{"initials":"JJ","lastname":"Luimstra","name":"Luimstra JJ"},{"initials":"K","lastname":"Wals","name":"Wals K"},{"initials":"M","lastname":"Toebes","name":"Toebes M"},{"initials":"L","lastname":"Bies","name":"Bies L"},{"initials":"R","lastname":"Ekkebus","name":"Ekkebus R"},{"initials":"P","lastname":"Rijal","name":"Rijal P"},{"initials":"PH","lastname":"Celie","name":"Celie PH"},{"initials":"JH","lastname":"Huang","name":"Huang JH"},{"initials":"ME","lastname":"Emmelot","name":"Emmelot ME"},{"initials":"RM","lastname":"Spaapen","name":"Spaapen RM"},{"initials":"H","lastname":"Lokhorst","name":"Lokhorst H"},{"initials":"TN","lastname":"Schumacher","name":"Schumacher TN"},{"initials":"T","lastname":"Mutis","name":"Mutis T"},{"initials":"B","lastname":"Rodenko","name":"Rodenko B"},{"initials":"H","lastname":"Ovaa","name":"Ovaa H"}],"identifier":[{"id":"10.4049/jimmunol.1400800","type":"doi"},{"id":"25311806","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"J. Immunol.","name":""},"pages":[null],"title":"Altered Peptide Ligands Revisited: Vaccine Design through Chemically Modified HLA-A2-Restricted T Cell Epitopes.","type":"article","url":"http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1400800","volume":[null],"year":[2014]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"1.65","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/4wj5"},"rcsb":{"url":"https://www.rcsb.org/structure/4wj5"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-A*02:01 binding \"XVAGIGILTX\" at 1.65&#8491; resolution","unique_chain_count":3}}
