{"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":"4mj6_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:35:55.149985"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":0.99,"sequence":"MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["A"],"match_type":"histo:assign_chains","score":0.91,"sequence":"GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW"},"peptide":{"chains":["C"],"match_type":"histo:classify_peptide","sequence":"TMVMELIRMIK"}},"chronology":{"deposition_date":"2013-09-03","deposition_year":2013,"release_date":"2014-10-08","release_year":2014,"revision_date":"2022-08-24","revision_year":2022},"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":"4MJ6 | HLA-A*11:01 binding \"TMVMELIRMIK\"","pdb_code":"4mj6","pdb_title":"Crystal structure of hla-a*1101 in complex with h7-22, an influenza a(h7n9) virus epitope","peptide":{"C":{"actual_length":11,"actual_sequence":"TMVMELIRMIK","chain_id":"C","features":["correct_sequence_and_length"],"full_length":11,"full_sequence":"TMVMELIRMIK"}},"peptide_length":11,"peptide_length_name":"undecamer","peptide_neighbours":{"1":{"neighbours":[{"position":67,"residue":"VAL"},{"position":9,"residue":"TYR"},{"position":163,"residue":"ARG"},{"position":7,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":66,"residue":"ASN"},{"position":45,"residue":"MET"},{"position":99,"residue":"TYR"},{"position":63,"residue":"GLU"}],"position":1,"residue":"THR"},"10":{"neighbours":[{"position":76,"residue":"VAL"},{"position":77,"residue":"ASP"},{"position":73,"residue":"THR"},{"position":143,"residue":"THR"},{"position":147,"residue":"TRP"},{"position":146,"residue":"LYS"}],"position":10,"residue":"ILE"},"11":{"neighbours":[{"position":77,"residue":"ASP"},{"position":124,"residue":"ILE"},{"position":116,"residue":"ASP"},{"position":81,"residue":"LEU"},{"position":80,"residue":"THR"},{"position":143,"residue":"THR"},{"position":147,"residue":"TRP"},{"position":84,"residue":"TYR"},{"position":95,"residue":"ILE"},{"position":142,"residue":"ILE"},{"position":146,"residue":"LYS"},{"position":114,"residue":"ARG"},{"position":97,"residue":"ILE"},{"position":123,"residue":"TYR"}],"position":11,"residue":"LYS"},"2":{"neighbours":[{"position":99,"residue":"TYR"},{"position":114,"residue":"ARG"},{"position":9,"residue":"TYR"},{"position":156,"residue":"GLN"},{"position":155,"residue":"GLN"},{"position":159,"residue":"TYR"},{"position":66,"residue":"ASN"}],"position":2,"residue":"MET"},"3":{"neighbours":[{"position":62,"residue":"GLN"},{"position":163,"residue":"ARG"},{"position":159,"residue":"TYR"},{"position":66,"residue":"ASN"}],"position":3,"residue":"VAL"},"4":{"neighbours":[{"position":66,"residue":"ASN"},{"position":114,"residue":"ARG"},{"position":156,"residue":"GLN"},{"position":69,"residue":"ALA"},{"position":70,"residue":"GLN"}],"position":4,"residue":"MET"},"6":{"neighbours":[{"position":155,"residue":"GLN"}],"position":6,"residue":"LEU"},"7":{"neighbours":[{"position":73,"residue":"THR"}],"position":7,"residue":"ILE"},"8":{"neighbours":[{"position":150,"residue":"ALA"},{"position":152,"residue":"ALA"},{"position":155,"residue":"GLN"},{"position":147,"residue":"TRP"}],"position":8,"residue":"ARG"},"9":{"neighbours":[{"position":114,"residue":"ARG"},{"position":152,"residue":"ALA"},{"position":147,"residue":"TRP"},{"position":156,"residue":"GLN"},{"position":133,"residue":"TRP"},{"position":73,"residue":"THR"},{"position":155,"residue":"GLN"},{"position":77,"residue":"ASP"},{"position":150,"residue":"ALA"}],"position":9,"residue":"MET"}},"peptide_sequence":"TMVMELIRMIK","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":"<h4>Background</h4>\u2003The emergence of infections by the novel avian influenza A(H7N9) virus has posed a threat to human health. Cross-immunity between A(H7N9) and other heterosubtypic influenza viruses affected by antigenicity-dependent substitutions needs to be investigated.<h4>Methods</h4>\u2003We investigated the cellular and humoral immune responses against A(H7N9) and 2009 pandemic influenza A(H1N1) virus (A[H1N1]pdm09), by serological and T-cell-specific assays, in a healthy population. The molecular bases of the cellular and humoral antigenic variability of A(H7N9) were illuminated by structural determination.<h4>Results</h4>\u2003We not only found that antibodies against A(H7N9) were lacking in the studied population, but also revealed that both CD4<sup>+</sup> and CD8<sup>+</sup> T cells that cross-reacted with A(H7N9) were at significantly lower levels than those against the A(H1N1)pdm09 peptides with substitutions. Moreover, individual peptides for A(H7N9) with low cross-reactivity were identified. Structural determination indicated that substitutions within these peptides influence the antigenic variability of A(H7N9) through both major histocompatibility complex (MHC) binding and T-cell receptor docking.<h4>Conclusions</h4>\u2003The impact of antigenicity-dependent substitutions on cross-reactivity of T-cell immunity against the novel influenza virus A(H7N9) in the healthy population benefits the understanding of immune evasion of influenza viruses and provides a useful reference for universal vaccine development.","bibjson":{"author":[{"initials":"WJ","lastname":"Liu","name":"Liu WJ"},{"initials":"S","lastname":"Tan","name":"Tan S"},{"initials":"M","lastname":"Zhao","name":"Zhao M"},{"initials":"C","lastname":"Quan","name":"Quan C"},{"initials":"Y","lastname":"Bi","name":"Bi Y"},{"initials":"Y","lastname":"Wu","name":"Wu Y"},{"initials":"S","lastname":"Zhang","name":"Zhang S"},{"initials":"H","lastname":"Zhang","name":"Zhang H"},{"initials":"H","lastname":"Xiao","name":"Xiao H"},{"initials":"J","lastname":"Qi","name":"Qi J"},{"initials":"J","lastname":"Yan","name":"Yan J"},{"initials":"W","lastname":"Liu","name":"Liu W"},{"initials":"H","lastname":"Yu","name":"Yu H"},{"initials":"Y","lastname":"Shu","name":"Shu Y"},{"initials":"G","lastname":"Wu","name":"Wu G"},{"initials":"GF","lastname":"Gao","name":"Gao GF"}],"identifier":[{"id":"10.1093/infdis/jiw471","type":"doi"},{"id":"27738054","type":"pubmed"}],"issue":["12"],"journal":{"iso_abbreviation":"J Infect Dis","name":""},"pages":["1937-1946"],"title":"Cross-immunity Against Avian Influenza A(H7N9) Virus in the Healthy Population Is Affected by Antigenicity-Dependent Substitutions.","type":"article","url":"https://academic.oup.com/jid/article-lookup/doi/10.1093/infdis/jiw471","volume":["214"],"year":[2016]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"2.57","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/4mj6"},"rcsb":{"url":"https://www.rcsb.org/structure/4mj6"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-A*11:01 binding \"TMVMELIRMIK\" at 2.57&#8491; resolution","unique_chain_count":3}}