{"display":true,"structure":{"allele":{"alpha":{"identifier":"uniprot:P01900","locus":"h2-d","match_type":"histo:fuzzy","name":"H2-Dd","slug":"h2_dd","species_stem":"H2"},"beta":{}},"assemblies":{"1":{"assembly_name":"3e6f_1","chains":["A","B","P"],"downloaded_at":"2022-11-09T14:45:35.389931"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":0.99,"sequence":"MQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM"},"class_i_alpha":{"chains":["A"],"match_type":"histo:assign_chains","score":0.88,"sequence":"MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLRTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRW"},"peptide":{"chains":["P"],"match_type":"histo:classify_peptide","sequence":"IGPGRAFYA"}},"chronology":{"deposition_date":"2008-08-15","deposition_year":2008,"release_date":"2009-08-18","release_year":2009,"revision_date":"2021-10-20","revision_year":2021},"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":"h2-d","manually_edited":{},"missing_residues":[],"page_title":"3E6F | H2-Dd binding \"IGPGRAFYA\"","pdb_code":"3e6f","pdb_title":"Mhc Class I h-2dd heavy chain complexed with beta-2 microglobulin and a variant peptide, pa9, from the human immunodeficiency virus (bal) envelope glycoprotein 120","peptide":{"P":{"actual_length":9,"actual_sequence":"IGPGRAFYA","chain_id":"P","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"IGPGRAFYA"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":171,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":164,"residue":"CYS"},{"position":163,"residue":"GLU"},{"position":63,"residue":"GLU"},{"position":159,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":66,"residue":"ARG"},{"position":5,"residue":"LEU"},{"position":167,"residue":"TRP"}],"position":1,"residue":"ILE"},"2":{"neighbours":[{"position":7,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":66,"residue":"ARG"},{"position":63,"residue":"GLU"}],"position":2,"residue":"GLY"},"3":{"neighbours":[{"position":7,"residue":"TYR"},{"position":70,"residue":"ASN"},{"position":159,"residue":"TYR"},{"position":99,"residue":"ALA"},{"position":66,"residue":"ARG"},{"position":114,"residue":"TRP"},{"position":97,"residue":"TRP"}],"position":3,"residue":"PRO"},"4":{"neighbours":[{"position":66,"residue":"ARG"},{"position":156,"residue":"ASP"},{"position":97,"residue":"TRP"},{"position":114,"residue":"TRP"},{"position":70,"residue":"ASN"}],"position":4,"residue":"GLY"},"5":{"neighbours":[{"position":77,"residue":"ASP"},{"position":116,"residue":"PHE"},{"position":114,"residue":"TRP"},{"position":74,"residue":"PHE"},{"position":97,"residue":"TRP"},{"position":73,"residue":"SER"},{"position":147,"residue":"TRP"},{"position":70,"residue":"ASN"}],"position":5,"residue":"ARG"},"6":{"neighbours":[{"position":155,"residue":"ARG"}],"position":6,"residue":"ALA"},"7":{"neighbours":[{"position":156,"residue":"ASP"},{"position":147,"residue":"TRP"},{"position":151,"residue":"GLY"},{"position":150,"residue":"ALA"},{"position":152,"residue":"ALA"},{"position":77,"residue":"ASP"},{"position":155,"residue":"ARG"}],"position":7,"residue":"PHE"},"8":{"neighbours":[{"position":143,"residue":"THR"},{"position":147,"residue":"TRP"},{"position":77,"residue":"ASP"},{"position":146,"residue":"LYS"},{"position":73,"residue":"SER"},{"position":76,"residue":"VAL"}],"position":8,"residue":"TYR"},"9":{"neighbours":[{"position":146,"residue":"LYS"},{"position":84,"residue":"TYR"},{"position":142,"residue":"ILE"},{"position":123,"residue":"TYR"},{"position":143,"residue":"THR"},{"position":80,"residue":"THR"},{"position":147,"residue":"TRP"},{"position":77,"residue":"ASP"}],"position":9,"residue":"ALA"}},"peptide_sequence":"IGPGRAFYA","pockets":{"a":{"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a163":{"number":163,"one_letter":"E","three_letter":"GLU"},"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":"E","three_letter":"GLU"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"Y","three_letter":"TYR"},"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":"N","three_letter":"ASN"},"a9":{"number":9,"one_letter":"V","three_letter":"VAL"},"a99":{"number":99,"one_letter":"A","three_letter":"ALA"}},"c":{"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"a73":{"number":73,"one_letter":"S","three_letter":"SER"},"a74":{"number":74,"one_letter":"F","three_letter":"PHE"},"a9":{"number":9,"one_letter":"V","three_letter":"VAL"},"a97":{"number":97,"one_letter":"W","three_letter":"TRP"}},"d":{"a114":{"number":114,"one_letter":"W","three_letter":"TRP"},"a155":{"number":155,"one_letter":"R","three_letter":"ARG"},"a156":{"number":156,"one_letter":"D","three_letter":"ASP"},"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":"W","three_letter":"TRP"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"A","three_letter":"ALA"},"a156":{"number":156,"one_letter":"D","three_letter":"ASP"},"a97":{"number":97,"one_letter":"W","three_letter":"TRP"}},"f":{"a116":{"number":116,"one_letter":"F","three_letter":"PHE"},"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":"A","three_letter":"ALA"},"a84":{"number":84,"one_letter":"Y","three_letter":"TYR"},"a95":{"number":95,"one_letter":"L","three_letter":"LEU"}}},"publication":{"abstract":"Prime-boost immunization with gene-based vectors has been developed to generate more effective vaccines for AIDS, malaria, and tuberculosis. Although these vectors elicit potent T cell responses, the mechanisms by which they stimulate immunity are not well understood. In this study, we show that immunization by a single gene product, HIV-1 envelope, with alternative vector combinations elicits CD8(+) cells with different fine specificities and kinetics of mobilization. Vaccine-induced CD8(+) T cells recognized overlapping third V region loop peptides. Unexpectedly, two anchor variants bound H-2D(d) better than the native sequences, and clones with distinct specificities were elicited by alternative vectors. X-ray crystallography revealed major differences in solvent exposure of MHC-bound peptide epitopes, suggesting that processed HIV-1 envelope gave rise to MHC-I/peptide conformations recognized by distinct CD8(+) T cell populations. These findings suggest that different gene-based vectors generate peptides with alternative conformations within MHC-I that elicit distinct T cell responses after vaccination.","bibjson":{"author":[{"initials":"M","lastname":"Honda","name":"Honda M"},{"initials":"R","lastname":"Wang","name":"Wang R"},{"initials":"WP","lastname":"Kong","name":"Kong WP"},{"initials":"M","lastname":"Kanekiyo","name":"Kanekiyo M"},{"initials":"W","lastname":"Akahata","name":"Akahata W"},{"initials":"L","lastname":"Xu","name":"Xu L"},{"initials":"K","lastname":"Matsuo","name":"Matsuo K"},{"initials":"K","lastname":"Natarajan","name":"Natarajan K"},{"initials":"H","lastname":"Robinson","name":"Robinson H"},{"initials":"TE","lastname":"Asher","name":"Asher TE"},{"initials":"DA","lastname":"Price","name":"Price DA"},{"initials":"DC","lastname":"Douek","name":"Douek DC"},{"initials":"DH","lastname":"Margulies","name":"Margulies DH"},{"initials":"GJ","lastname":"Nabel","name":"Nabel GJ"}],"identifier":[{"id":"10.4049/jimmunol.0900581","type":"doi"},{"id":"19620307","type":"pubmed"}],"issue":["4"],"journal":{"iso_abbreviation":"J. Immunol.","name":""},"pages":["2425-34"],"title":"Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity.","type":"article","url":"http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.0900581","volume":["183"],"year":[2009]},"in_pmc":"Y","in_pmce":"Y","open_access":"N"},"resolution":"2.41","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/3e6f"},"rcsb":{"url":"https://www.rcsb.org/structure/3e6f"}},"species":{"common_name":"Mouse","match_type":"histo:assign_species","scientific_name":"Mus musculus","slug":"mus_musculus"},"tcr":null,"title":"H2-Dd binding \"IGPGRAFYA\" at 2.41&#8491; resolution","unique_chain_count":3}}
