{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA32458","locus":"hla-b","match_type":"histo:exact","name":"HLA-B*39:01","slug":"hla_b_39_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"4o2e_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:28:29.028330"},"2":{"assembly_name":"4o2e_2","chains":["D","E","F"],"downloaded_at":"2022-11-09T14:28:29.564897"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B","E"],"match_type":"histo:assign_chains","score":1.0,"sequence":"IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["A","D"],"match_type":"histo:assign_chains","score":0.94,"sequence":"GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQICKTNTQTDRESLRNLRGYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHNQFAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRTYLEGTCVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW"},"peptide":{"chains":["C","F"],"match_type":"histo:classify_peptide","sequence":"SHVAVENAL"}},"chronology":{"deposition_date":"2013-12-17","deposition_year":2013,"release_date":"2014-07-23","release_year":2014,"revision_date":"2014-07-23","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-b","manually_edited":{},"missing_residues":[],"page_title":"4O2E | HLA-B*39:01 binding \"SHVAVENAL\"","pdb_code":"4o2e","pdb_title":"A peptide complexed with hla-b*3901","peptide":{"C":{"actual_length":9,"actual_sequence":"SHVAVENAL","chain_id":"C","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"SHVAVENAL"},"F":{"actual_length":9,"actual_sequence":"SHVAVENAL","chain_id":"F","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"SHVAVENAL"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":59,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":5,"residue":"MET"},{"position":99,"residue":"TYR"},{"position":63,"residue":"ASN"},{"position":159,"residue":"TYR"},{"position":167,"residue":"TRP"},{"position":33,"residue":"PHE"},{"position":62,"residue":"ARG"},{"position":171,"residue":"TYR"}],"position":1,"residue":"SER"},"2":{"neighbours":[{"position":34,"residue":"VAL"},{"position":159,"residue":"TYR"},{"position":67,"residue":"CYS"},{"position":70,"residue":"ASN"},{"position":9,"residue":"TYR"},{"position":45,"residue":"GLU"},{"position":7,"residue":"TYR"},{"position":99,"residue":"TYR"},{"position":24,"residue":"SER"},{"position":63,"residue":"ASN"},{"position":66,"residue":"ILE"}],"position":2,"residue":"HIS"},"3":{"neighbours":[{"position":99,"residue":"TYR"},{"position":156,"residue":"LEU"},{"position":66,"residue":"ILE"},{"position":159,"residue":"TYR"},{"position":97,"residue":"ARG"},{"position":9,"residue":"TYR"}],"position":3,"residue":"VAL"},"4":{"neighbours":[{"position":66,"residue":"ILE"}],"position":4,"residue":"ALA"},"5":{"neighbours":[{"position":152,"residue":"VAL"},{"position":155,"residue":"GLN"},{"position":70,"residue":"ASN"},{"position":97,"residue":"ARG"},{"position":156,"residue":"LEU"}],"position":5,"residue":"VAL"},"6":{"neighbours":[{"position":69,"residue":"THR"},{"position":73,"residue":"THR"},{"position":70,"residue":"ASN"}],"position":6,"residue":"GLU"},"7":{"neighbours":[{"position":155,"residue":"GLN"},{"position":73,"residue":"THR"},{"position":147,"residue":"TRP"},{"position":150,"residue":"ALA"},{"position":77,"residue":"SER"},{"position":152,"residue":"VAL"}],"position":7,"residue":"ASN"},"8":{"neighbours":[{"position":146,"residue":"LYS"},{"position":147,"residue":"TRP"},{"position":77,"residue":"SER"},{"position":80,"residue":"ASN"},{"position":73,"residue":"THR"},{"position":76,"residue":"GLU"},{"position":143,"residue":"THR"}],"position":8,"residue":"ALA"},"9":{"neighbours":[{"position":95,"residue":"LEU"},{"position":147,"residue":"TRP"},{"position":143,"residue":"THR"},{"position":77,"residue":"SER"},{"position":146,"residue":"LYS"},{"position":116,"residue":"PHE"},{"position":81,"residue":"LEU"},{"position":123,"residue":"TYR"},{"position":80,"residue":"ASN"},{"position":84,"residue":"TYR"}],"position":9,"residue":"LEU"}},"peptide_sequence":"SHVAVENAL","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":"N","three_letter":"ASN"},"a66":{"number":66,"one_letter":"I","three_letter":"ILE"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"S","three_letter":"SER"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"E","three_letter":"GLU"},"a63":{"number":63,"one_letter":"N","three_letter":"ASN"},"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":"N","three_letter":"ASN"},"a9":{"number":9,"one_letter":"Y","three_letter":"TYR"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"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":"R","three_letter":"ARG"}},"d":{"a114":{"number":114,"one_letter":"N","three_letter":"ASN"},"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":"N","three_letter":"ASN"},"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":"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":"S","three_letter":"SER"},"a80":{"number":80,"one_letter":"N","three_letter":"ASN"},"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":"As one of the most common posttranslational modifications (PTMs) of eukaryotic proteins, N(\u03b1)-terminal acetylation (Nt-acetylation) generates a class of N(\u03b1)-acetylpeptides that are known to be presented by MHC class I at the cell surface. Although such PTM plays a pivotal role in adjusting proteolysis, the molecular basis for the presentation and T cell recognition of N(\u03b1)-acetylpeptides remains largely unknown. In this study, we determined a high-resolution crystallographic structure of HLA (HLA)-B*3901 complexed with an N(\u03b1)-acetylpeptide derived from natural cellular processing, also in comparison with the unmodified-peptide complex. Unlike the \u03b1-amino-free P1 residues of unmodified peptide, of which the \u03b1-amino group inserts into pocket A of the Ag-binding groove, the N(\u03b1)-linked acetyl of the acetylated P1-Ser protrudes out of the groove for T cell recognition. Moreover, the Nt-acetylation not only alters the conformation of the peptide but also switches the residues in the \u03b11-helix of HLA-B*3901, which may impact the T cell engagement. The thermostability measurements of complexes between N(\u03b1)-acetylpeptides and a series of MHC class I molecules derived from different species reveal reduced stability. Our findings provide the insight into the mode of N(\u03b1)-acetylpeptide-specific presentation by classical MHC class I molecules and shed light on the potential of acetylepitope-based immune intervene and vaccine development.","bibjson":{"author":[{"initials":"M","lastname":"Sun","name":"Sun M"},{"initials":"J","lastname":"Liu","name":"Liu J"},{"initials":"J","lastname":"Qi","name":"Qi J"},{"initials":"B","lastname":"Tefsen","name":"Tefsen B"},{"initials":"Y","lastname":"Shi","name":"Shi Y"},{"initials":"J","lastname":"Yan","name":"Yan J"},{"initials":"GF","lastname":"Gao","name":"Gao GF"}],"identifier":[{"id":"10.4049/jimmunol.1400199","type":"doi"},{"id":"24829406","type":"pubmed"}],"issue":["12"],"journal":{"iso_abbreviation":"J. Immunol.","name":""},"pages":["5509-19"],"title":"N\ufffd\ufffd-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted n\ufffd\ufffd-acetylpeptide presentation.","type":"article","url":"http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1400199","volume":["192"],"year":[2014]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"1.98","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/4o2e"},"rcsb":{"url":"https://www.rcsb.org/structure/4o2e"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-B*39:01 binding \"SHVAVENAL\" at 1.98Å resolution","unique_chain_count":3}}