{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-mhc:SLA06150","locus":"sla-2","match_type":"histo:exact","name":"SLA-2*04:02","slug":"sla_2_04_02","species_stem":"SLA"},"beta":{}},"assemblies":{"1":{"assembly_name":"6a6h_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:44:56.313701"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":0.99,"sequence":"VARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH"},"class_i_alpha":{"chains":["A"],"match_type":"histo:assign_chains","score":0.88,"sequence":"GPHSLRYFDTAVSRPDRGEPRFIEVGYVDDTQFVRFDSDAPNPRMEPRAPWIQQEGQEYWDRNTRNAMGNAQIYRGNLRTALGYYNQSEAGSHTLQIMYGCDVGPDGLLLRGYSQDAYDGADYIALNEDLRSWTAADTAAQITKRKWEAANVAEQWRSYLQGTCVEWLQKYLQMGKDTLQRAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGTFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD"},"peptide":{"chains":["C"],"match_type":"histo:classify_peptide","sequence":"MTAHIVVPY"}},"chronology":{"deposition_date":"2018-06-28","deposition_year":2018,"release_date":"2019-07-03","release_year":2019,"revision_date":"2020-01-15","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":"sla-2","manually_edited":{},"missing_residues":[],"page_title":"6A6H | SLA-2*04:02 binding \"MTAHIVVPY\"","pdb_code":"6a6h","pdb_title":"Crystal structure of swine major histocompatibility complex Class I sla-2*040202 for 2.3 angstrom","peptide":{"C":{"actual_length":9,"actual_sequence":"MTAHIVVPY","chain_id":"C","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"MTAHIVVPY"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":159,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":167,"residue":"TRP"},{"position":7,"residue":"TYR"},{"position":5,"residue":"LEU"},{"position":171,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":63,"residue":"ASN"},{"position":66,"residue":"ASN"},{"position":33,"residue":"PHE"},{"position":163,"residue":"THR"}],"position":1,"residue":"MET"},"2":{"neighbours":[{"position":63,"residue":"ASN"},{"position":66,"residue":"ASN"},{"position":163,"residue":"THR"},{"position":24,"residue":"GLU"},{"position":159,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":62,"residue":"ARG"},{"position":67,"residue":"ALA"},{"position":45,"residue":"MET"},{"position":99,"residue":"TYR"}],"position":2,"residue":"THR"},"3":{"neighbours":[{"position":156,"residue":"TRP"},{"position":99,"residue":"TYR"},{"position":70,"residue":"ASN"},{"position":66,"residue":"ASN"},{"position":159,"residue":"TYR"}],"position":3,"residue":"ALA"},"4":{"neighbours":[{"position":66,"residue":"ASN"},{"position":155,"residue":"GLN"}],"position":4,"residue":"HIS"},"5":{"neighbours":[{"position":152,"residue":"VAL"},{"position":156,"residue":"TRP"},{"position":155,"residue":"GLN"},{"position":159,"residue":"TYR"},{"position":73,"residue":"ILE"},{"position":70,"residue":"ASN"}],"position":5,"residue":"ILE"},"6":{"neighbours":[{"position":155,"residue":"GLN"},{"position":73,"residue":"ILE"},{"position":70,"residue":"ASN"}],"position":6,"residue":"VAL"},"7":{"neighbours":[{"position":155,"residue":"GLN"},{"position":146,"residue":"LYS"},{"position":73,"residue":"ILE"},{"position":152,"residue":"VAL"},{"position":147,"residue":"TRP"},{"position":150,"residue":"ALA"}],"position":7,"residue":"VAL"},"8":{"neighbours":[{"position":77,"residue":"ASN"},{"position":73,"residue":"ILE"},{"position":146,"residue":"LYS"}],"position":8,"residue":"PRO"},"9":{"neighbours":[{"position":81,"residue":"ALA"},{"position":146,"residue":"LYS"},{"position":77,"residue":"ASN"},{"position":73,"residue":"ILE"},{"position":143,"residue":"THR"},{"position":84,"residue":"TYR"},{"position":147,"residue":"TRP"},{"position":95,"residue":"LEU"},{"position":80,"residue":"THR"},{"position":123,"residue":"TYR"}],"position":9,"residue":"TYR"}},"peptide_sequence":"MTAHIVVPY","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":"L","three_letter":"LEU"},"a59":{"number":59,"one_letter":"Y","three_letter":"TYR"},"a63":{"number":63,"one_letter":"N","three_letter":"ASN"},"a66":{"number":66,"one_letter":"N","three_letter":"ASN"},"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":"M","three_letter":"MET"},"a63":{"number":63,"one_letter":"N","three_letter":"ASN"},"a66":{"number":66,"one_letter":"N","three_letter":"ASN"},"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":"D","three_letter":"ASP"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"a73":{"number":73,"one_letter":"I","three_letter":"ILE"},"a74":{"number":74,"one_letter":"Y","three_letter":"TYR"},"a9":{"number":9,"one_letter":"D","three_letter":"ASP"},"a97":{"number":97,"one_letter":"I","three_letter":"ILE"}},"d":{"a114":{"number":114,"one_letter":"S","three_letter":"SER"},"a155":{"number":155,"one_letter":"Q","three_letter":"GLN"},"a156":{"number":156,"one_letter":"W","three_letter":"TRP"},"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":"S","three_letter":"SER"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"V","three_letter":"VAL"},"a156":{"number":156,"one_letter":"W","three_letter":"TRP"},"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":"N","three_letter":"ASN"},"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":"Presentation of viral epitopes by swine MHC I (termed leukocyte antigen class I, SLA I) to cytotoxic T lymphocytes (CTLs) is crucial for swine immunity. The SLA-2 structure, however, remains largely unknown. To illustrate the structural basis of swine CTL epitope presentation, the crystal structure of SLA-2*04:02:02 complexed with one peptide, derived from foot-and-mouth disease virus (FMDV), was analyzed in this study. SLA-2*04:02:02 and swine \u03b22-microglobulin (s\u03b22m) were refolded in vitro in the presence of peptides. X-ray diffraction data of SLA-2*04:02:02-peptide-s\u03b22m (referred to as p/SLA-2*04:02:02) were collected. The diffraction dataset was 2.3\u202f\u00c5 in resolution and the space group was P3(2)21. Relevant data included a\u202f=\u202f101.8\u202f\u00c5, b\u202f=\u202f101.8\u202f\u00c5, c\u202f=\u202f73.455\u202f\u00c5,\u03b1\u202f=\u202f90.00\u00b0, \u03b2\u202f=\u202f90.00\u00b0, \u03b3\u202f=\u202f120.00\u00b0. The structure of p/SLA-2*04:02:02 was analyzed. The results revealed that Glu24, Met68, Gly76, and Gln173 in PBG of SLA-2*04:02:02 are different from other MHC I. Furthermore, Asn63 is different from other SLA I. Gln57, Met174 and Gln180 in PBG of SLA I are different from other species' MHC I. All of these features are different from known mammalian peptide-MHC class I complexes (referred to as p/MHC I). In addition, P4-His, P6-Val, and P8-Pro in the peptide were exposed, and these residues as epitopes can be presented by SLA-2*04:02:02. This study not only provides a structural basis for peptide presentation by SLA-2, but also screens one potential FMDV CTL epitope. The results may be of interest in future vaccine development.","bibjson":{"author":[{"initials":"S","lastname":"Ning","name":"Ning S"},{"initials":"ZB","lastname":"Wang","name":"Wang ZB"},{"initials":"P","lastname":"Qi","name":"Qi P"},{"initials":"J","lastname":"Xiao","name":"Xiao J"},{"initials":"XJ","lastname":"Wang","name":"Wang XJ"}],"identifier":[{"id":"10.1016/j.rvsc.2019.11.002","type":"doi"},{"id":"31760318","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"Res. Vet. Sci.","name":""},"pages":["90-98"],"title":"Crystallization of SLA-2*04:02:02 complexed with a CTL epitope derived from FMDV.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S0034528819303285","volume":["128"],"year":[2019]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"2.31","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6a6h"},"rcsb":{"url":"https://www.rcsb.org/structure/6a6h"}},"species":{"common_name":"Feral Pig","match_type":"histo:assign_species","scientific_name":"Sus scrofa","slug":"sus_scrofa"},"tcr":null,"title":"SLA-2*04:02 binding \"MTAHIVVPY\" at 2.31Å resolution","unique_chain_count":3}}