{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA31685","locus":"hla-b","match_type":"histo:exact","name":"HLA-B*27:247","slug":"hla_b_27_247","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"5def_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:38:36.974827"}},"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":0.99,"sequence":"GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYWDRETQICKAKAQTDRESLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAAREAEQLRAYLEGECVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPGEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP"},"peptide":{"chains":["C"],"match_type":"histo:classify_peptide","sequence":"RRKWRRWHL"}},"chronology":{"deposition_date":"2015-08-25","deposition_year":2015,"release_date":"2015-11-18","release_year":2015,"revision_date":"2020-04-22","revision_year":2020},"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":"5DEF | HLA-B*27:247 binding \"RRKWRRWHL\"","pdb_code":"5def","pdb_title":"Crystal structure of b*27:04 complex bound to the pvipr peptide","peptide":{"C":{"actual_length":9,"actual_sequence":"RRKWRRWHL","chain_id":"C","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"RRKWRRWHL"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":163,"residue":"GLU"},{"position":63,"residue":"GLU"},{"position":167,"residue":"TRP"},{"position":5,"residue":"MET"},{"position":171,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":7,"residue":"TYR"}],"position":1,"residue":"ARG"},"2":{"neighbours":[{"position":67,"residue":"CYS"},{"position":9,"residue":"HIS"},{"position":159,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":26,"residue":"GLY"},{"position":99,"residue":"TYR"},{"position":24,"residue":"THR"},{"position":7,"residue":"TYR"},{"position":25,"residue":"VAL"},{"position":66,"residue":"ILE"},{"position":163,"residue":"GLU"},{"position":63,"residue":"GLU"},{"position":34,"residue":"VAL"},{"position":45,"residue":"GLU"}],"position":2,"residue":"ARG"},"3":{"neighbours":[{"position":66,"residue":"ILE"},{"position":99,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":155,"residue":"GLN"},{"position":156,"residue":"LEU"},{"position":114,"residue":"HIS"}],"position":3,"residue":"LYS"},"4":{"neighbours":[{"position":62,"residue":"ARG"},{"position":65,"residue":"GLN"},{"position":66,"residue":"ILE"}],"position":4,"residue":"TRP"},"5":{"neighbours":[{"position":155,"residue":"GLN"},{"position":156,"residue":"LEU"},{"position":152,"residue":"GLU"}],"position":5,"residue":"ARG"},"6":{"neighbours":[{"position":155,"residue":"GLN"},{"position":69,"residue":"ALA"},{"position":152,"residue":"GLU"},{"position":70,"residue":"LYS"},{"position":66,"residue":"ILE"},{"position":73,"residue":"THR"}],"position":6,"residue":"ARG"},"7":{"neighbours":[{"position":73,"residue":"THR"},{"position":150,"residue":"ALA"},{"position":146,"residue":"LYS"},{"position":152,"residue":"GLU"},{"position":147,"residue":"TRP"}],"position":7,"residue":"TRP"},"8":{"neighbours":[{"position":73,"residue":"THR"},{"position":76,"residue":"GLU"},{"position":77,"residue":"SER"},{"position":143,"residue":"THR"},{"position":146,"residue":"LYS"},{"position":147,"residue":"TRP"}],"position":8,"residue":"HIS"},"9":{"neighbours":[{"position":81,"residue":"LEU"},{"position":142,"residue":"ILE"},{"position":77,"residue":"SER"},{"position":80,"residue":"THR"},{"position":116,"residue":"ASP"},{"position":95,"residue":"LEU"},{"position":146,"residue":"LYS"},{"position":84,"residue":"TYR"},{"position":147,"residue":"TRP"},{"position":143,"residue":"THR"},{"position":123,"residue":"TYR"},{"position":124,"residue":"ILE"}],"position":9,"residue":"LEU"}},"peptide_sequence":"RRKWRRWHL","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":"E","three_letter":"GLU"},"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":"S","three_letter":"SER"},"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":"<h4>Objective</h4>Dissimilarities in antigen processing and presentation are known to contribute to the differential association of HLA-B*27 subtypes with the inflammatory rheumatic disease ankylosing spondylitis (AS). In support of this notion, previous x-ray crystallographic data showed that peptides can be displayed by almost identical HLA-B*27 molecules in a subtype-dependent manner, allowing cytotoxic T lymphocytes to distinguish between these subtypes. For example, a human self-peptide derived from vasoactive intestinal peptide receptor type 1 (pVIPR; sequence RRKWRRWHL) is displayed in a single conformation by B*27:09 (which is not associated with AS), while B*27:05 (which is associated with AS) presents the peptide in a dual binding mode. In addition, differences in conformational flexibility between these subtypes might affect their stability or antigen presentation capability. This study was undertaken to investigate B*27:04 and B*27:06, another pair of minimally distinct HLA-B*27 subtypes, to assess whether dual peptide conformations or structural dynamics play a role in the initiation of AS.<h4>Methods</h4>Using x-ray crystallography, we determined the structures of the pVIPR-B*27:04 and pVIPR-B*27:06 complexes and used isotope-edited infrared (IR) spectroscopy to probe the dynamics of these HLA-B*27 subtypes.<h4>Results</h4>As opposed to B*27:05 and B*27:09, B*27:04 (which is associated with AS) displays pVIPR conventionally and B*27:06 (which is not associated with AS) presents the peptide in a dual conformation. Comparison of the 4 HLA-B*27 subtypes using IR spectroscopy revealed that B*27:04 and B*27:05 possess elevated molecular dynamics compared to the nonassociated subtypes B*27:06 and B*27:09.<h4>Conclusion</h4>Our results demonstrate that an increase in conformational flexibility characterizes the disease-associated subtypes B*27:04 and B*27:05.","bibjson":{"author":[{"initials":"B","lastname":"Loll","name":"Loll B"},{"initials":"H","lastname":"Fabian","name":"Fabian H"},{"initials":"H","lastname":"Huser","name":"Huser H"},{"initials":"CS","lastname":"Hee","name":"Hee CS"},{"initials":"A","lastname":"Ziegler","name":"Ziegler A"},{"initials":"B","lastname":"Uchanska-Ziegler","name":"Uchanska-Ziegler B"},{"initials":"A","lastname":"Ziegler","name":"Ziegler A"}],"identifier":[{"id":"10.1002/art.39567","type":"doi"},{"id":"26748477","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":null,"name":""},"pages":[null],"title":"Increased conformational flexibility characterizes HLA-B*27 subtypes associated with ankylosing spondylitis.","type":"article","url":"https://onlinelibrary.wiley.com/doi/10.1002/art.39567","volume":[null],"year":[2016]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"1.60","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/5def"},"rcsb":{"url":"https://www.rcsb.org/structure/5def"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-B*27:247 binding \"RRKWRRWHL\" at 1.60&#8491; resolution","unique_chain_count":3}}