{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA35266","locus":"hla-a","match_type":"histo:exact","name":"HLA-A*02:01","slug":"hla_a_02_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"6ss9_1","chains":["A","B","C"],"downloaded_at":"2022-11-09T14:29:39.911869"},"2":{"assembly_name":"6ss9_2","chains":["D","E","F"],"downloaded_at":"2022-11-09T14:29:40.340089"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B","E"],"match_type":"histo:assign_chains","score":0.99,"sequence":"MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["A","D"],"match_type":"histo:assign_chains","score":1.0,"sequence":"GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP"},"peptide":{"chains":["C","F"],"match_type":"histo:classify_peptide","sequence":"LLWNGPMHV"}},"chronology":{"deposition_date":"2019-09-06","deposition_year":2019,"release_date":"2020-07-15","release_year":2020,"revision_date":"2020-07-22","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-a","manually_edited":{},"missing_residues":[],"page_title":"6SS9 | HLA-A*02:01 binding \"LLWNGPMHV\"","pdb_code":"6ss9","pdb_title":"Human leukocyte antigen Class I a02 carrying LLWNGPMHV","peptide":{"C":{"actual_length":9,"actual_sequence":"LLWNGPMHV","chain_id":"C","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"LLWNGPMHV"},"F":{"actual_length":9,"actual_sequence":"LLWNGPMHV","chain_id":"F","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"LLWNGPMHV"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":159,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":7,"residue":"TYR"},{"position":171,"residue":"TYR"},{"position":163,"residue":"THR"},{"position":63,"residue":"GLU"},{"position":5,"residue":"MET"},{"position":167,"residue":"TRP"},{"position":33,"residue":"PHE"}],"position":1,"residue":"LEU"},"2":{"neighbours":[{"position":70,"residue":"HIS"},{"position":7,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":9,"residue":"PHE"},{"position":66,"residue":"LYS"},{"position":63,"residue":"GLU"},{"position":67,"residue":"VAL"},{"position":99,"residue":"TYR"},{"position":45,"residue":"MET"}],"position":2,"residue":"LEU"},"3":{"neighbours":[{"position":66,"residue":"LYS"},{"position":99,"residue":"TYR"},{"position":114,"residue":"HIS"},{"position":155,"residue":"GLN"},{"position":97,"residue":"ARG"},{"position":70,"residue":"HIS"},{"position":156,"residue":"LEU"},{"position":152,"residue":"VAL"},{"position":159,"residue":"TYR"}],"position":3,"residue":"TRP"},"4":{"neighbours":[{"position":66,"residue":"LYS"},{"position":155,"residue":"GLN"}],"position":4,"residue":"ASN"},"5":{"neighbours":[{"position":155,"residue":"GLN"}],"position":5,"residue":"GLY"},"6":{"neighbours":[{"position":73,"residue":"THR"},{"position":97,"residue":"ARG"},{"position":70,"residue":"HIS"},{"position":69,"residue":"ALA"},{"position":155,"residue":"GLN"}],"position":6,"residue":"PRO"},"7":{"neighbours":[{"position":73,"residue":"THR"},{"position":77,"residue":"ASP"},{"position":152,"residue":"VAL"},{"position":147,"residue":"TRP"},{"position":150,"residue":"ALA"},{"position":146,"residue":"LYS"},{"position":97,"residue":"ARG"}],"position":7,"residue":"MET"},"8":{"neighbours":[{"position":77,"residue":"ASP"},{"position":147,"residue":"TRP"},{"position":143,"residue":"THR"},{"position":146,"residue":"LYS"},{"position":72,"residue":"GLN"},{"position":76,"residue":"VAL"},{"position":73,"residue":"THR"}],"position":8,"residue":"HIS"},"9":{"neighbours":[{"position":116,"residue":"TYR"},{"position":80,"residue":"THR"},{"position":84,"residue":"TYR"},{"position":77,"residue":"ASP"},{"position":147,"residue":"TRP"},{"position":123,"residue":"TYR"},{"position":142,"residue":"THR"},{"position":143,"residue":"THR"},{"position":146,"residue":"LYS"},{"position":81,"residue":"LEU"}],"position":9,"residue":"VAL"}},"peptide_sequence":"LLWNGPMHV","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":"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":"H","three_letter":"HIS"},"a9":{"number":9,"one_letter":"F","three_letter":"PHE"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"H","three_letter":"HIS"},"a73":{"number":73,"one_letter":"T","three_letter":"THR"},"a74":{"number":74,"one_letter":"H","three_letter":"HIS"},"a9":{"number":9,"one_letter":"F","three_letter":"PHE"},"a97":{"number":97,"one_letter":"R","three_letter":"ARG"}},"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":"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":"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":"D","three_letter":"ASP"},"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":"V","three_letter":"VAL"}}},"publication":{"abstract":"The CD8 T cell response to the HLA-A2-restricted epitope LLWNGPMAV (LLW) of the non-structural protein 4b of Yellow Fever Virus (YFV) is remarkably immunodominant, highly prevalent and powerful in YFV-vaccinated humans. Here we used a combinatorial peptide library screening in the context of an A2/LLW-specific CD8 T cell clone to identify a superagonist that features a methionine to isoleucine substitution at position 7. Based on in silico modeling, the functional enhancement of this LLW-7I mutation was associated with alterations in the structural dynamics of the peptide in the major histocompatibility complex (pMHC) binding with the T cell receptor (TCR). While the TCR off-rate of LLW-7I pMHC is comparable to the wild type peptide, the rigidity of the 7I peptide seems to confer less entropy loss upon TCR binding. This LLW-7I superagonist is an example of improved functionality in human CD8 T cells associated with optimized ligand rigidity for TCR binding and not with changes in TCR:pMHC off-rate kinetics.","bibjson":{"author":[{"initials":"A","lastname":"Bovay","name":"Bovay A"},{"initials":"V","lastname":"Zoete","name":"Zoete V"},{"initials":"PJ","lastname":"Rizkallah","name":"Rizkallah PJ"},{"initials":"K","lastname":"Beck","name":"Beck K"},{"initials":"P","lastname":"Delbreil","name":"Delbreil P"},{"initials":"DE","lastname":"Speiser","name":"Speiser DE"},{"initials":"DK","lastname":"Cole","name":"Cole DK"},{"initials":"SA","lastname":"Fuertes Marraco","name":"Fuertes Marraco SA"}],"identifier":[{"id":"10.1016/j.molimm.2020.06.025","type":"doi"},{"id":"32645549","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":"Mol. Immunol.","name":""},"pages":["43-50"],"title":"Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b <sub>214-222</sub> by combinatorial peptide library screening.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S016158902030403X","volume":["125"],"year":[2020]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"2.70","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6ss9"},"rcsb":{"url":"https://www.rcsb.org/structure/6ss9"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-A*02:01 binding \"LLWNGPMHV\" at 2.70&#8491; resolution","unique_chain_count":3}}
