{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA34703","locus":"hla-b","match_type":"histo:exact","name":"HLA-B*40:01","slug":"hla_b_40_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"6iex_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:30:12.703135"}},"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":0.92,"sequence":"GSHSMRYFHTAMSRPGRGEPRFITVGYVDDTLFVRFDSDATSPRKEPRAPWIEQEGPEYWDRETQISKTNTQTYRESLRNLRGYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHNQYAYDGKDYIALNEDLRSWTAADTAAQISQRKLEAARVAEQLRAYLEGECVEWLRRYLENGKDKLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW"},"peptide":{"chains":["C"],"match_type":"histo:classify_peptide","sequence":"GETALALLLL"}},"chronology":{"deposition_date":"2018-09-17","deposition_year":2018,"release_date":"2019-09-18","release_year":2019,"revision_date":"2021-03-31","revision_year":2021},"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":"6IEX | HLA-B*40:01 binding \"GETALALLLL\"","pdb_code":"6iex","pdb_title":"Crystal structure of hla-b*4001 in complex with sars-cov derived peptide n216-225 GETALALLLL","peptide":{"C":{"actual_length":10,"actual_sequence":"GETALALLLL","chain_id":"C","features":["correct_sequence_and_length"],"full_length":10,"full_sequence":"GETALALLLL"}},"peptide_length":10,"peptide_length_name":"decamer","peptide_neighbours":{"1":{"neighbours":[{"position":62,"residue":"ARG"},{"position":7,"residue":"TYR"},{"position":163,"residue":"GLU"},{"position":59,"residue":"TYR"},{"position":63,"residue":"GLU"},{"position":171,"residue":"TYR"},{"position":167,"residue":"TRP"},{"position":5,"residue":"MET"},{"position":159,"residue":"TYR"}],"position":1,"residue":"GLY"},"10":{"neighbours":[{"position":77,"residue":"SER"},{"position":116,"residue":"TYR"},{"position":76,"residue":"GLU"},{"position":80,"residue":"ASN"},{"position":84,"residue":"TYR"},{"position":147,"residue":"LEU"},{"position":143,"residue":"SER"},{"position":123,"residue":"TYR"},{"position":95,"residue":"LEU"},{"position":124,"residue":"ILE"},{"position":146,"residue":"LYS"},{"position":81,"residue":"LEU"}],"position":10,"residue":"LEU"},"2":{"neighbours":[{"position":159,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":24,"residue":"THR"},{"position":62,"residue":"ARG"},{"position":70,"residue":"ASN"},{"position":45,"residue":"LYS"},{"position":99,"residue":"TYR"},{"position":9,"residue":"HIS"},{"position":163,"residue":"GLU"},{"position":63,"residue":"GLU"},{"position":66,"residue":"ILE"},{"position":67,"residue":"SER"}],"position":2,"residue":"GLU"},"3":{"neighbours":[{"position":99,"residue":"TYR"},{"position":156,"residue":"LEU"},{"position":66,"residue":"ILE"},{"position":159,"residue":"TYR"},{"position":97,"residue":"ARG"}],"position":3,"residue":"THR"},"4":{"neighbours":[{"position":62,"residue":"ARG"},{"position":66,"residue":"ILE"}],"position":4,"residue":"ALA"},"5":{"neighbours":[{"position":156,"residue":"LEU"},{"position":155,"residue":"GLN"},{"position":70,"residue":"ASN"}],"position":5,"residue":"LEU"},"6":{"neighbours":[{"position":69,"residue":"THR"},{"position":70,"residue":"ASN"},{"position":66,"residue":"ILE"},{"position":73,"residue":"THR"}],"position":6,"residue":"ALA"},"7":{"neighbours":[{"position":73,"residue":"THR"},{"position":69,"residue":"THR"},{"position":70,"residue":"ASN"}],"position":7,"residue":"LEU"},"8":{"neighbours":[{"position":77,"residue":"SER"},{"position":116,"residue":"TYR"},{"position":156,"residue":"LEU"},{"position":147,"residue":"LEU"},{"position":152,"residue":"VAL"},{"position":97,"residue":"ARG"},{"position":73,"residue":"THR"}],"position":8,"residue":"LEU"},"9":{"neighbours":[{"position":73,"residue":"THR"},{"position":76,"residue":"GLU"},{"position":80,"residue":"ASN"},{"position":147,"residue":"LEU"},{"position":77,"residue":"SER"},{"position":146,"residue":"LYS"}],"position":9,"residue":"LEU"}},"peptide_sequence":"GETALALLLL","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":"K","three_letter":"LYS"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"I","three_letter":"ILE"},"a67":{"number":67,"one_letter":"S","three_letter":"SER"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"a9":{"number":9,"one_letter":"H","three_letter":"HIS"},"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":"Y","three_letter":"TYR"},"a9":{"number":9,"one_letter":"H","three_letter":"HIS"},"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":"L","three_letter":"LEU"},"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":"Y","three_letter":"TYR"},"a123":{"number":123,"one_letter":"Y","three_letter":"TYR"},"a143":{"number":143,"one_letter":"S","three_letter":"SER"},"a146":{"number":146,"one_letter":"K","three_letter":"LYS"},"a147":{"number":147,"one_letter":"L","three_letter":"LEU"},"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":"The viral peptides presentation by major histocompatibility complex class I (MHC I) molecules play a pivotal role in T-cell recognition and the subsequent virus clearance. This process is delicately adjusted by the variant residues of MHC I, especially the residues in the peptide binding groove (PBG). In a series of MHC I molecules, a salt bridge is formed above the N-terminus of the peptides. However, the potential impact of the salt bridge on peptide binding and T-cell receptor (TCR) recognition of MHC I, as well as the corresponding molecular basis, are still largely unknown. Herein, we determined the structures of HLA-B*4001 and H-2K<sup>d</sup> in which two different types of salt bridges (Arg62-Glu163 or Arg66-Glu163) across the PBG were observed. Although the two salt bridges led to different conformation shifts of both the MHC I \u03b1 helix and the peptides, binding of the peptides with the salt bridge residues was relatively conserved. Furthermore, through a series of in vitro and in vivo investigations, we found that MHC I mutations that disrupt the salt bridge alleviate peptide binding and can weaken the TCR recognition of MHC I-peptide complexes. Our study may provide key references for understanding MHC I-restricted peptide recognition by T-cells.","bibjson":{"author":[{"initials":"W","lastname":"Ji","name":"Ji W"},{"initials":"L","lastname":"Niu","name":"Niu L"},{"initials":"W","lastname":"Peng","name":"Peng W"},{"initials":"Y","lastname":"Zhang","name":"Zhang Y"},{"initials":"H","lastname":"Cheng","name":"Cheng H"},{"initials":"F","lastname":"Gao","name":"Gao F"},{"initials":"Y","lastname":"Shi","name":"Shi Y"},{"initials":"J","lastname":"Qi","name":"Qi J"},{"initials":"GF","lastname":"Gao","name":"Gao GF"},{"initials":"WJ","lastname":"Liu","name":"Liu WJ"}],"identifier":[{"id":"10.1016/j.molimm.2019.06.005","type":"doi"},{"id":"31226552","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"Mol Immunol","name":""},"pages":["274-282"],"title":"Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S0161589019300860","volume":["112"],"year":[2019]},"in_pmc":"N","in_pmce":"Y","open_access":"Y"},"resolution":"2.31","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6iex"},"rcsb":{"url":"https://www.rcsb.org/structure/6iex"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-B*40:01 binding \"GETALALLLL\" at 2.31&#8491; resolution","unique_chain_count":3}}