{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-mhc:SLA06131","locus":"sla-1","match_type":"histo:exact","name":"SLA-1*13:01","slug":"sla_1_13_01","species_stem":"SLA"},"beta":{}},"assemblies":{"1":{"assembly_name":"6lf9_1","chains":["D","E","F"],"downloaded_at":"2022-11-09T14:40:44.452538"},"2":{"assembly_name":"6lf9_2","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:40:44.933872"},"3":{"assembly_name":"6lf9_3","chains":["G","H","I"],"downloaded_at":"2022-11-09T14:40:45.245600"},"4":{"assembly_name":"6lf9_4","chains":["J","K","L"],"downloaded_at":"2022-11-09T14:40:45.535213"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["E","B","H","K"],"match_type":"histo:assign_chains","score":0.99,"sequence":"ARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH"},"class_i_alpha":{"chains":["D","A","G","J"],"match_type":"histo:assign_chains","score":0.97,"sequence":"GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDNYAPNPRMEPRVPWIQQEGQDYWDEETRKVKDNAQTYGVGLNTLRGYYNQSEAGSHTLQSMFGCYLGPDGLLLHGYRQDAYDGADYIALNEDLRSWTAADMAAQITKRKWEAANVAERRRSYLQGLCVESLRRYLEMGKDTLQRAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGTFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLR"},"peptide":{"chains":["F","C","I","L"],"match_type":"histo:classify_peptide","sequence":"RVEDVTNTAEYW"}},"chronology":{"deposition_date":"2019-11-30","deposition_year":2019,"release_date":"2021-03-17","release_year":2021,"revision_date":"2022-03-23","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":"sla-1","manually_edited":{},"missing_residues":[],"page_title":"6LF9 | SLA-1*13:01 binding \"RVEDVTNTAEYW\"","pdb_code":"6lf9","pdb_title":"Crystal structure of psla-1*1301 complex with dodecapeptide RVEDVTNTAEYW","peptide":{"C":{"actual_length":12,"actual_sequence":"RVEDVTNTAEYW","chain_id":"C","features":["correct_sequence_and_length"],"full_length":12,"full_sequence":"RVEDVTNTAEYW"},"F":{"actual_length":12,"actual_sequence":"RVEDVTNTAEYW","chain_id":"F","features":["correct_sequence_and_length"],"full_length":12,"full_sequence":"RVEDVTNTAEYW"},"I":{"actual_length":12,"actual_sequence":"RVEDVTNTAEYW","chain_id":"I","features":["correct_sequence_and_length"],"full_length":12,"full_sequence":"RVEDVTNTAEYW"},"L":{"actual_length":12,"actual_sequence":"RVEDVTNTAEYW","chain_id":"L","features":["correct_sequence_and_length"],"full_length":12,"full_sequence":"RVEDVTNTAEYW"}},"peptide_length":12,"peptide_length_name":"dodecamer","peptide_neighbours":{"1":{"neighbours":[{"position":66,"residue":"LYS"},{"position":55,"residue":"GLU"},{"position":63,"residue":"GLU"},{"position":167,"residue":"SER"},{"position":171,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":62,"residue":"GLU"},{"position":163,"residue":"LEU"},{"position":170,"residue":"ARG"}],"position":1,"residue":"ARG"},"10":{"neighbours":[{"position":72,"residue":"GLN"},{"position":69,"residue":"ASP"},{"position":76,"residue":"VAL"},{"position":73,"residue":"THR"}],"position":10,"residue":"GLU"},"11":{"neighbours":[{"position":146,"residue":"LYS"},{"position":73,"residue":"THR"},{"position":147,"residue":"TRP"},{"position":152,"residue":"VAL"},{"position":143,"residue":"THR"},{"position":150,"residue":"ALA"}],"position":11,"residue":"TYR"},"12":{"neighbours":[{"position":73,"residue":"THR"},{"position":97,"residue":"SER"},{"position":123,"residue":"TYR"},{"position":146,"residue":"LYS"},{"position":81,"residue":"LEU"},{"position":147,"residue":"TRP"},{"position":95,"residue":"LEU"},{"position":80,"residue":"THR"},{"position":114,"residue":"ARG"},{"position":84,"residue":"TYR"},{"position":77,"residue":"GLY"},{"position":124,"residue":"ILE"},{"position":143,"residue":"THR"},{"position":74,"residue":"TYR"},{"position":116,"residue":"ASP"}],"position":12,"residue":"TRP"},"2":{"neighbours":[{"position":59,"residue":"TYR"},{"position":163,"residue":"LEU"},{"position":7,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":33,"residue":"PHE"},{"position":63,"residue":"GLU"},{"position":167,"residue":"SER"},{"position":5,"residue":"LEU"},{"position":171,"residue":"TYR"},{"position":159,"residue":"TYR"}],"position":2,"residue":"VAL"},"3":{"neighbours":[{"position":34,"residue":"VAL"},{"position":159,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":70,"residue":"ASN"},{"position":9,"residue":"TYR"},{"position":163,"residue":"LEU"},{"position":45,"residue":"MET"},{"position":99,"residue":"PHE"},{"position":63,"residue":"GLU"},{"position":66,"residue":"LYS"},{"position":67,"residue":"VAL"}],"position":3,"residue":"GLU"},"4":{"neighbours":[{"position":70,"residue":"ASN"},{"position":155,"residue":"ARG"},{"position":66,"residue":"LYS"},{"position":99,"residue":"PHE"},{"position":156,"residue":"ARG"},{"position":159,"residue":"TYR"}],"position":4,"residue":"ASP"},"5":{"neighbours":[{"position":65,"residue":"ARG"},{"position":62,"residue":"GLU"},{"position":66,"residue":"LYS"}],"position":5,"residue":"VAL"},"6":{"neighbours":[{"position":156,"residue":"ARG"},{"position":69,"residue":"ASP"},{"position":73,"residue":"THR"},{"position":70,"residue":"ASN"}],"position":6,"residue":"THR"},"7":{"neighbours":[{"position":155,"residue":"ARG"}],"position":7,"residue":"ASN"},"8":{"neighbours":[{"position":155,"residue":"ARG"}],"position":8,"residue":"THR"},"9":{"neighbours":[{"position":155,"residue":"ARG"},{"position":73,"residue":"THR"}],"position":9,"residue":"ALA"}},"peptide_sequence":"RVEDVTNTAEYW","pockets":{"a":{"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a163":{"number":163,"one_letter":"L","three_letter":"LEU"},"a167":{"number":167,"one_letter":"S","three_letter":"SER"},"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":"K","three_letter":"LYS"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"A","three_letter":"ALA"},"a34":{"number":34,"one_letter":"V","three_letter":"VAL"},"a45":{"number":45,"one_letter":"M","three_letter":"MET"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"K","three_letter":"LYS"},"a67":{"number":67,"one_letter":"V","three_letter":"VAL"},"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":"F","three_letter":"PHE"}},"c":{"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"a73":{"number":73,"one_letter":"T","three_letter":"THR"},"a74":{"number":74,"one_letter":"Y","three_letter":"TYR"},"a9":{"number":9,"one_letter":"Y","three_letter":"TYR"},"a97":{"number":97,"one_letter":"S","three_letter":"SER"}},"d":{"a114":{"number":114,"one_letter":"R","three_letter":"ARG"},"a155":{"number":155,"one_letter":"R","three_letter":"ARG"},"a156":{"number":156,"one_letter":"R","three_letter":"ARG"},"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a160":{"number":160,"one_letter":"L","three_letter":"LEU"},"a99":{"number":99,"one_letter":"F","three_letter":"PHE"}},"e":{"a114":{"number":114,"one_letter":"R","three_letter":"ARG"},"a147":{"number":147,"one_letter":"W","three_letter":"TRP"},"a152":{"number":152,"one_letter":"V","three_letter":"VAL"},"a156":{"number":156,"one_letter":"R","three_letter":"ARG"},"a97":{"number":97,"one_letter":"S","three_letter":"SER"}},"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":"G","three_letter":"GLY"},"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":"Polymorphisms can affect MHC-I binding peptide length preferences, but the mechanism remains unclear. Using a random peptide library combined with LC-MS/MS and <i>de novo</i> sequencing (RPLD-MS) technique, we found that two swine MHC-I molecules with high sequence homology, SLA-1*04:01 and SLA-1*13:01, had significant differences in length preference of the binding peptides. Compared with SLA-1*04:01, SLA-1*13:01 binds fewer short peptides with 8-10 amino acids, but more long peptides. A dodecapeptide peptide (RW12) can bind to both SLA-1*04:01 and SLA-1*13:01, but their crystal structures indicate that the binding modes are significantly different: the entirety of RW12 is embedded in the peptide binding groove of SLA-1*04:01, but it obviously protrudes from the peptide binding groove of SLA-1*13:01. The structural comparative analysis showed that only five differential amino acids of SLA-1*13:01 and SLA-1*04:01 were involved in the binding of RW12, and they determine the different ways of long peptides binding, which makes SLA-1*04:01 more restrictive on long peptides than SLA-1*13:01, and thus binds fewer long peptides. In addition, we found that the N terminus of RW12 extends from the groove of SLA-1*13:01, which is similar to the case previously found in SLA-1*04:01. However, this unusual peptide binding does not affect their preferences of binding peptide length. Our study will be helpful to understand the effect of polymorphisms on the length distribution of MHC-I binding peptides, and to screen SLA-I-restricted epitopes of different lengths and to design effective epitope vaccines.","bibjson":{"author":[{"initials":null,"lastname":null,"name":"Wei, X.H."},{"initials":null,"lastname":null,"name":"Wang, S."},{"initials":null,"lastname":null,"name":"Zhang, N.Z."},{"initials":null,"lastname":null,"name":"Xia, C."}],"identifier":[{"id":"10.3389/fimmu.2022.820881","type":"doi"}],"issue":[null],"journal":{"iso_abbreviation":null,"name":""},"pages":["-"],"title":"Peptidomes and Structures Illustrate How SLA-I Micropolymorphism Influences the Preference of Binding Peptide Length.","type":"article","url":"https://www.frontiersin.org/articles/10.3389/fimmu.2022.820881/full","volume":[null],"year":[2022]},"in_pmc":"N","in_pmce":"Y","open_access":"Y"},"resolution":"2.50","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6lf9"},"rcsb":{"url":"https://www.rcsb.org/structure/6lf9"}},"species":{"common_name":"Feral Pig","match_type":"histo:assign_species","scientific_name":"Sus scrofa","slug":"sus_scrofa"},"tcr":null,"title":"SLA-1*13:01 binding \"RVEDVTNTAEYW\" at 2.50&#8491; resolution","unique_chain_count":3}}