{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA34811","locus":"hla-b","match_type":"histo:exact","name":"HLA-B*27:05","slug":"hla_b_27_05","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"6vqz_1","chains":["A","B","F"],"downloaded_at":"2022-11-09T14:39:24.297200"},"2":{"assembly_name":"6vqz_2","chains":["C","D","G"],"downloaded_at":"2022-11-09T14:39:25.216357"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B","D"],"match_type":"histo:assign_chains","score":1.0,"sequence":"IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["A","C"],"match_type":"histo:assign_chains","score":1.0,"sequence":"GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYWDRETQICKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP"},"peptide":{"chains":["G","F"],"match_type":"histo:classify_peptide","sequence":"KRWIIL"}},"chronology":{"deposition_date":"2020-02-06","deposition_year":2020,"release_date":"2021-02-10","release_year":2021,"revision_date":"2022-03-09","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-b","manually_edited":{},"missing_residues":[],"page_title":"6VQZ | HLA-B*27:05 binding \"KRWIIL\"","pdb_code":"6vqz","pdb_title":"Hla-b*27:05 presenting an hiv-1 6mer peptide","peptide":{"F":{"actual_length":6,"actual_sequence":"KRWIIL","chain_id":"F","features":["correct_sequence_and_length","short_peptide"],"full_length":6,"full_sequence":"KRWIIL"},"G":{"actual_length":6,"actual_sequence":"KRWIIL","chain_id":"G","features":["correct_sequence_and_length","short_peptide"],"full_length":6,"full_sequence":"KRWIIL"}},"peptide_length":6,"peptide_length_name":"hexamer","peptide_neighbours":{"1":{"neighbours":[{"position":171,"residue":"TYR"},{"position":33,"residue":"PHE"},{"position":7,"residue":"TYR"},{"position":163,"residue":"GLU"},{"position":5,"residue":"MET"},{"position":159,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":59,"residue":"TYR"},{"position":63,"residue":"GLU"},{"position":66,"residue":"ILE"},{"position":167,"residue":"TRP"}],"position":1,"residue":"LYS"},"2":{"neighbours":[{"position":36,"residue":"PHE"},{"position":45,"residue":"GLU"},{"position":8,"residue":"PHE"},{"position":67,"residue":"CYS"},{"position":26,"residue":"GLY"},{"position":25,"residue":"VAL"},{"position":9,"residue":"HIS"},{"position":34,"residue":"VAL"},{"position":7,"residue":"TYR"},{"position":163,"residue":"GLU"},{"position":24,"residue":"THR"},{"position":99,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":63,"residue":"GLU"},{"position":35,"residue":"ARG"},{"position":66,"residue":"ILE"}],"position":2,"residue":"ARG"},"3":{"neighbours":[{"position":66,"residue":"ILE"},{"position":114,"residue":"HIS"},{"position":152,"residue":"VAL"},{"position":99,"residue":"TYR"},{"position":155,"residue":"GLN"},{"position":156,"residue":"LEU"},{"position":159,"residue":"TYR"}],"position":3,"residue":"TRP"},"4":{"neighbours":[{"position":70,"residue":"LYS"},{"position":155,"residue":"GLN"},{"position":69,"residue":"ALA"},{"position":65,"residue":"GLN"},{"position":62,"residue":"ARG"},{"position":66,"residue":"ILE"}],"position":4,"residue":"ILE"},"5":{"neighbours":[{"position":152,"residue":"VAL"},{"position":155,"residue":"GLN"},{"position":147,"residue":"TRP"},{"position":73,"residue":"THR"}],"position":5,"residue":"ILE"},"6":{"neighbours":[{"position":155,"residue":"GLN"}],"position":6,"residue":"LEU"}},"peptide_sequence":"KRWIIL","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":"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":"I","three_letter":"ILE"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"T","three_letter":"THR"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"E","three_letter":"GLU"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"I","three_letter":"ILE"},"a67":{"number":67,"one_letter":"C","three_letter":"CYS"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"K","three_letter":"LYS"},"a9":{"number":9,"one_letter":"H","three_letter":"HIS"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"K","three_letter":"LYS"},"a73":{"number":73,"one_letter":"T","three_letter":"THR"},"a74":{"number":74,"one_letter":"D","three_letter":"ASP"},"a9":{"number":9,"one_letter":"H","three_letter":"HIS"},"a97":{"number":97,"one_letter":"N","three_letter":"ASN"}},"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":"N","three_letter":"ASN"}},"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":"L","three_letter":"LEU"}}},"publication":{"abstract":"Cytotoxic T lymphocyte (CTL) and natural killer (NK) cell responses to a single optimal 10-mer epitope (KK10) in the human immunodeficiency virus type-1 (HIV-1) protein p24Gag are associated with enhanced immune control in patients expressing human leukocyte antigen (HLA)-B<sup>\u2217</sup>27:05. We find that proteasomal activity generates multiple length variants of KK10 (4-14 amino acids), which bind TAP and HLA-B<sup>\u2217</sup>27:05. However, only epitope forms \u22658 amino acids evoke peptide length-specific and cross-reactive CTL responses. Structural analyses reveal that all epitope forms bind HLA-B<sup>\u2217</sup>27:05 via a conserved N-terminal motif, and competition experiments show that the truncated epitope forms outcompete immunogenic epitope forms for binding to HLA-B<sup>\u2217</sup>27:05. Common viral escape mutations abolish (L136M) or impair (R132K) production of KK10 and longer epitope forms. Peptide length influences how well the inhibitory NK cell receptor KIR3DL1 binds HLA-B<sup>\u2217</sup>27:05 peptide complexes and how intraepitope mutations affect this interaction. These results identify a viral escape mechanism from CTL and NK responses based on differential antigen processing and peptide competition.","bibjson":{"author":[{"initials":null,"lastname":null,"name":"Pymm, P."},{"initials":null,"lastname":null,"name":"Tenzer, S."},{"initials":null,"lastname":null,"name":"Wee, E."},{"initials":null,"lastname":null,"name":"Weimershaus, M."},{"initials":null,"lastname":null,"name":"Burgevin, A."},{"initials":null,"lastname":null,"name":"Kollnberger, S."},{"initials":null,"lastname":null,"name":"Gerstoft, J."},{"initials":null,"lastname":null,"name":"Josephs, T.M."},{"initials":null,"lastname":null,"name":"Ladell, K."},{"initials":null,"lastname":null,"name":"McLaren, J.E."},{"initials":null,"lastname":null,"name":"Appay, V."},{"initials":null,"lastname":null,"name":"Price, D.A."},{"initials":null,"lastname":null,"name":"Fugger, L."},{"initials":null,"lastname":null,"name":"Bell, J.I."},{"initials":null,"lastname":null,"name":"Schild, H."},{"initials":null,"lastname":null,"name":"van Endert, P."},{"initials":null,"lastname":null,"name":"Harkiolaki, M."},{"initials":null,"lastname":null,"name":"Iversen, A.K."}],"identifier":[{"id":"10.1016/j.celrep.2022.110449","type":"doi"}],"issue":[null],"journal":{"iso_abbreviation":null,"name":""},"pages":["-"],"title":"Epitope length variants balance protective immune responses and viral escape in HIV-1 infection","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S2211124722001760","volume":["38"],"year":[2022]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"2.25","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6vqz"},"rcsb":{"url":"https://www.rcsb.org/structure/6vqz"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-B*27:05 binding \"KRWIIL\" at 2.25&#8491; resolution","unique_chain_count":3}}