{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA35265","locus":"hla-c","match_type":"histo:exact","name":"HLA-C*05:01","slug":"hla_c_05_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"7su9_1","chains":["D","E","A","B","C"],"downloaded_at":"2022-11-09T14:28:00.153594"}},"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":0.98,"sequence":"CSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVQFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQTDRVNLRKLRGYYNQSEAGSHTLQRMYGCDLGPDGRLLRGYNQFAYDGKDYIALNEDLRSWTAADKAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKKTLQRAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWGPSSQP"},"peptide":{"chains":["C"],"match_type":"histo:classify_peptide","sequence":"GADGVGKSL"},"tcr_alpha":{"chains":["D"],"match_type":"stcrdab","sequence":"MAGLAKTTQPISVDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEVASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGDMDQAGTALIFGKGTTLSVSSDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSP","subgroup":"TRAV4"},"tcr_beta":{"chains":["E"],"match_type":"stcrdab","sequence":"MAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLGEGRVDGYTFGSGTRLTVVEDLRNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD","subgroup":"TRBV5"}},"chronology":{"deposition_date":"2021-11-16","deposition_year":2021,"release_date":"2022-06-08","release_year":2022,"revision_date":"2022-06-08","revision_year":2022},"class":"class_i","classical":true,"complex_type":"class_i_with_peptide_and_alpha_beta_tcr","components":["class_i_alpha","beta2m","peptide","tcr_alpha","tcr_beta"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"hla-c","manually_edited":{},"missing_residues":[],"page_title":"7SU9 | HLA-C*05:01 presenting \"GADGVGKSL\" to Alpha/Beta T cell receptor","pdb_code":"7su9","pdb_title":"Kras-g12d specific TCR9a in complex with c*05-GADGVGKSL","peptide":{"C":{"actual_length":9,"actual_sequence":"GADGVGKSL","chain_id":"C","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"GADGVGKSL"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":5,"residue":"MET"},{"position":171,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":7,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":63,"residue":"GLU"},{"position":167,"residue":"TRP"},{"position":33,"residue":"PHE"},{"position":159,"residue":"TYR"}],"position":1,"residue":"GLY"},"2":{"neighbours":[{"position":99,"residue":"TYR"},{"position":63,"residue":"GLU"},{"position":167,"residue":"TRP"},{"position":67,"residue":"TYR"},{"position":9,"residue":"TYR"},{"position":159,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":7,"residue":"TYR"}],"position":2,"residue":"ALA"},"3":{"neighbours":[{"position":99,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":156,"residue":"ARG"},{"position":97,"residue":"ARG"},{"position":9,"residue":"TYR"},{"position":159,"residue":"TYR"}],"position":3,"residue":"ASP"},"4":{"neighbours":[{"position":66,"residue":"LYS"},{"position":97,"residue":"ARG"},{"position":156,"residue":"ARG"},{"position":70,"residue":"GLN"}],"position":4,"residue":"GLY"},"5":{"neighbours":[{"position":66,"residue":"LYS"},{"position":156,"residue":"ARG"},{"position":69,"residue":"ARG"},{"position":73,"residue":"THR"},{"position":70,"residue":"GLN"}],"position":5,"residue":"VAL"},"6":{"neighbours":[{"position":156,"residue":"ARG"},{"position":73,"residue":"THR"},{"position":152,"residue":"GLU"}],"position":6,"residue":"GLY"},"7":{"neighbours":[{"position":146,"residue":"LYS"},{"position":156,"residue":"ARG"},{"position":150,"residue":"ALA"},{"position":147,"residue":"TRP"},{"position":152,"residue":"GLU"}],"position":7,"residue":"LYS"},"8":{"neighbours":[{"position":76,"residue":"VAL"},{"position":73,"residue":"THR"},{"position":147,"residue":"TRP"},{"position":80,"residue":"LYS"},{"position":77,"residue":"ASN"},{"position":146,"residue":"LYS"}],"position":8,"residue":"SER"},"9":{"neighbours":[{"position":146,"residue":"LYS"},{"position":84,"residue":"TYR"},{"position":95,"residue":"LEU"},{"position":123,"residue":"TYR"},{"position":147,"residue":"TRP"},{"position":80,"residue":"LYS"},{"position":116,"residue":"PHE"},{"position":81,"residue":"LEU"},{"position":77,"residue":"ASN"},{"position":143,"residue":"THR"}],"position":9,"residue":"LEU"}},"peptide_sequence":"GADGVGKSL","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":"G","three_letter":"GLY"},"a63":{"number":63,"one_letter":"E","three_letter":"GLU"},"a66":{"number":66,"one_letter":"K","three_letter":"LYS"},"a67":{"number":67,"one_letter":"Y","three_letter":"TYR"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"Q","three_letter":"GLN"},"a9":{"number":9,"one_letter":"Y","three_letter":"TYR"},"a99":{"number":99,"one_letter":"Y","three_letter":"TYR"}},"c":{"a70":{"number":70,"one_letter":"Q","three_letter":"GLN"},"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":"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":"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":"E","three_letter":"GLU"},"a156":{"number":156,"one_letter":"R","three_letter":"ARG"},"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":"N","three_letter":"ASN"},"a80":{"number":80,"one_letter":"K","three_letter":"LYS"},"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":"Dimorphic amino acids at positions 77 and 80 delineate HLA-C allotypes into two groups, C1 and C2, which associate with disease through interactions with C1 and C2-specific natural killer cell receptors. How the C1/C2 dimorphism affects T cell recognition is unknown. Using HLA-C allotypes that differ only by the C1/C2-defining residues, we found that KRAS-G12D neoantigen-specific T cell receptors (TCRs) discriminated between C1 and C2 presenting the same KRAS-G12D peptides. Structural and functional experiments, and immunopeptidomics analysis revealed that Ser77 in C1 and Asn77 in C2 influence amino acid preference near the peptide C-terminus (p\u03a9), including the p\u03a9-1 position, in which C1 favors small and C2 prefers large residues. This resulted in weaker TCR affinity for KRAS-G12D-bound C2-HLA-C despite conserved TCR contacts. Thus, the C1/C2 dimorphism on its own impacts peptide presentation and HLA-C-restricted T cell responses, with implications in disease, including adoptive T cell therapy targeting KRAS-G12D-induced cancers.","bibjson":{"author":[{"initials":null,"lastname":null,"name":"Sim, M.J.W."},{"initials":null,"lastname":null,"name":"Stotz, Z."},{"initials":null,"lastname":null,"name":"Lu, J."},{"initials":null,"lastname":null,"name":"Brennan, P."},{"initials":null,"lastname":null,"name":"Long, E.O."},{"initials":null,"lastname":null,"name":"Sun, P.D."}],"identifier":[{"id":"10.7554/eLife.75670","type":"doi"},{"id":"35587797","type":"pubmed"}],"issue":[null],"journal":{"iso_abbreviation":null,"name":""},"pages":["-"],"title":"T cells discriminate between groups C1 and C2 HLA-C.","type":"article","url":"https://elifesciences.org/articles/75670","volume":["11"],"year":[2022]},"in_pmc":"N","in_pmce":"Y","open_access":"Y"},"resolution":"1.99","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/7su9"},"rcsb":{"url":"https://www.rcsb.org/structure/7su9"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=7su9"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":{"alpha":{"chains":["D"],"subgroup":"TRAV4"},"beta":{"chains":["E"],"subgroup":"TRBV5"},"pdb_code":"7su9"},"title":"HLA-C*05:01 presenting \"GADGVGKSL\" to Alpha/Beta T cell receptor at 1.99&#8491; resolution","unique_chain_count":5}}
