{"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":"7phr_1","chains":["A","B","C","D","E","e","H","L","P","Z","z"],"downloaded_at":"2022-11-09T14:43:24.086910"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["L"],"match_type":"histo:assign_chains","score":0.99,"sequence":"MGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM"},"class_i_alpha":{"chains":["H"],"match_type":"histo:assign_chains","score":0.95,"sequence":"MGSSHHHHHHGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSSQPEDQVDPRLIDGK"},"peptide":{"chains":["P"],"match_type":"histo:classify_peptide","sequence":"YLEPGPVTV"},"tcr_alpha":{"chains":["A"],"match_type":"stcrdab","sequence":"MSQQGEEDPQALSIQEGENATMNCSYKTSINNLQWYRQNSGRGLVHLILIRSNEREKHSGRLRVTLDTSKKSSSLLITASRAADTASYFCATDGSTPMQFGKGTRLSVIPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS","subgroup":"TRAV17"},"tcr_beta":{"chains":["B"],"match_type":"stcrdab","sequence":"MDGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSWAQGDFQKGDIAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSWGAPYEQYFGPGTRLTVTEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADCGFTSVSYQQGVLSATILYEILLGKATLYAVLVSALVLMAMVKRKDF","subgroup":"TRBV19"}},"chronology":{"deposition_date":"2021-08-18","deposition_year":2021,"release_date":"2022-08-31","release_year":2022,"revision_date":"2022-08-31","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":"Electron Microscopy","facets":{},"ligands":[],"locus":"hla-a","manually_edited":{},"missing_residues":[],"page_title":"7PHR | HLA-A*02:01 presenting \"YLEPGPVTV\" to Alpha/Beta T cell receptor","pdb_code":"7phr","pdb_title":"Structure of a fully assembled t-cell receptor engaging a tumor-associated peptide-MHC i","peptide":{"P":{"actual_length":9,"actual_sequence":"YLEPGPVTV","chain_id":"P","features":["correct_sequence_and_length"],"full_length":9,"full_sequence":"YLEPGPVTV"}},"peptide_length":9,"peptide_length_name":"nonamer","peptide_neighbours":{"1":{"neighbours":[{"position":163,"residue":"THR"},{"position":167,"residue":"TRP"},{"position":159,"residue":"TYR"},{"position":59,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":33,"residue":"PHE"},{"position":5,"residue":"MET"},{"position":99,"residue":"TYR"},{"position":63,"residue":"GLU"},{"position":66,"residue":"LYS"},{"position":171,"residue":"TYR"}],"position":1,"residue":"TYR"},"2":{"neighbours":[{"position":45,"residue":"MET"},{"position":99,"residue":"TYR"},{"position":63,"residue":"GLU"},{"position":66,"residue":"LYS"},{"position":67,"residue":"VAL"},{"position":159,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":70,"residue":"HIS"},{"position":9,"residue":"PHE"}],"position":2,"residue":"LEU"},"3":{"neighbours":[{"position":70,"residue":"HIS"},{"position":156,"residue":"LEU"},{"position":155,"residue":"GLN"},{"position":99,"residue":"TYR"},{"position":66,"residue":"LYS"},{"position":159,"residue":"TYR"}],"position":3,"residue":"GLU"},"4":{"neighbours":[{"position":66,"residue":"LYS"},{"position":155,"residue":"GLN"},{"position":70,"residue":"HIS"},{"position":69,"residue":"ALA"}],"position":4,"residue":"PRO"},"5":{"neighbours":[{"position":70,"residue":"HIS"},{"position":69,"residue":"ALA"}],"position":5,"residue":"GLY"},"6":{"neighbours":[{"position":97,"residue":"ARG"},{"position":73,"residue":"THR"},{"position":70,"residue":"HIS"},{"position":69,"residue":"ALA"}],"position":6,"residue":"PRO"},"7":{"neighbours":[{"position":150,"residue":"ALA"},{"position":146,"residue":"LYS"},{"position":152,"residue":"VAL"},{"position":97,"residue":"ARG"},{"position":73,"residue":"THR"},{"position":77,"residue":"ASP"},{"position":147,"residue":"TRP"}],"position":7,"residue":"VAL"},"8":{"neighbours":[{"position":146,"residue":"LYS"},{"position":77,"residue":"ASP"},{"position":73,"residue":"THR"},{"position":76,"residue":"VAL"},{"position":147,"residue":"TRP"}],"position":8,"residue":"THR"},"9":{"neighbours":[{"position":123,"residue":"TYR"},{"position":146,"residue":"LYS"},{"position":77,"residue":"ASP"},{"position":80,"residue":"THR"},{"position":84,"residue":"TYR"},{"position":147,"residue":"TRP"},{"position":143,"residue":"THR"},{"position":81,"residue":"LEU"},{"position":142,"residue":"THR"},{"position":116,"residue":"TYR"}],"position":9,"residue":"VAL"}},"peptide_sequence":"YLEPGPVTV","pockets":{"a":{"a159":{"number":159,"one_letter":"W","three_letter":"TRP"},"a163":{"number":163,"one_letter":"H","three_letter":"HIS"},"a167":{"number":167,"one_letter":"Q","three_letter":"GLN"},"a171":{"number":171,"one_letter":"Y","three_letter":"TYR"},"a5":{"number":5,"one_letter":"H","three_letter":"HIS"},"a59":{"number":59,"one_letter":"P","three_letter":"PRO"},"a63":{"number":63,"one_letter":"W","three_letter":"TRP"},"a66":{"number":66,"one_letter":"Q","three_letter":"GLN"},"a7":{"number":7,"one_letter":"H","three_letter":"HIS"}},"b":{"a24":{"number":24,"one_letter":"V","three_letter":"VAL"},"a34":{"number":34,"one_letter":"F","three_letter":"PHE"},"a45":{"number":45,"one_letter":"F","three_letter":"PHE"},"a63":{"number":63,"one_letter":"W","three_letter":"TRP"},"a66":{"number":66,"one_letter":"Q","three_letter":"GLN"},"a67":{"number":67,"one_letter":"E","three_letter":"GLU"},"a7":{"number":7,"one_letter":"H","three_letter":"HIS"},"a70":{"number":70,"one_letter":"E","three_letter":"GLU"},"a9":{"number":9,"one_letter":"H","three_letter":"HIS"},"a99":{"number":99,"one_letter":"Q","three_letter":"GLN"}},"c":{"a70":{"number":70,"one_letter":"E","three_letter":"GLU"},"a73":{"number":73,"one_letter":"D","three_letter":"ASP"},"a74":{"number":74,"one_letter":"G","three_letter":"GLY"},"a9":{"number":9,"one_letter":"H","three_letter":"HIS"},"a97":{"number":97,"one_letter":"Y","three_letter":"TYR"}},"d":{"a114":{"number":114,"one_letter":"D","three_letter":"ASP"},"a155":{"number":155,"one_letter":"T","three_letter":"THR"},"a156":{"number":156,"one_letter":"K","three_letter":"LYS"},"a159":{"number":159,"one_letter":"W","three_letter":"TRP"},"a160":{"number":160,"one_letter":"E","three_letter":"GLU"},"a99":{"number":99,"one_letter":"Q","three_letter":"GLN"}},"e":{"a114":{"number":114,"one_letter":"D","three_letter":"ASP"},"a147":{"number":147,"one_letter":"A","three_letter":"ALA"},"a152":{"number":152,"one_letter":"A","three_letter":"ALA"},"a156":{"number":156,"one_letter":"K","three_letter":"LYS"},"a97":{"number":97,"one_letter":"Y","three_letter":"TYR"}},"f":{"a116":{"number":116,"one_letter":"G","three_letter":"GLY"},"a123":{"number":123,"one_letter":"R","three_letter":"ARG"},"a143":{"number":143,"one_letter":"R","three_letter":"ARG"},"a146":{"number":146,"one_letter":"T","three_letter":"THR"},"a147":{"number":147,"one_letter":"A","three_letter":"ALA"},"a77":{"number":77,"one_letter":"R","three_letter":"ARG"},"a80":{"number":80,"one_letter":"K","three_letter":"LYS"},"a81":{"number":81,"one_letter":"A","three_letter":"ALA"},"a84":{"number":84,"one_letter":"Q","three_letter":"GLN"},"a95":{"number":95,"one_letter":"G","three_letter":"GLY"}}},"publication":{"abstract":"The T\u00a0cell receptor (TCR) expressed by T lymphocytes initiates protective immune responses to pathogens and tumors. To explore the structural basis of how TCR signaling is initiated when the receptor binds to peptide-loaded major histocompatibility complex (pMHC) molecules, we used cryogenic electron microscopy to determine the structure of a tumor-reactive TCR\u03b1\u03b2/CD3\u03b4\u03b3\u03b5<sub>2</sub>\u03b6<sub>2</sub> complex bound to a melanoma-specific human class I pMHC at 3.08\u00a0\u00c5 resolution. The antigen-bound complex comprises 11 subunits stabilized by multivalent interactions across three structural layers, with clustered membrane-proximal cystines stabilizing the CD3-\u03b5\u03b4 and CD3-\u03b5\u03b3 heterodimers. Extra density sandwiched between transmembrane helices reveals the involvement of sterol lipids in TCR assembly. The geometry of the pMHC/TCR complex suggests that efficient TCR scanning of pMHC requires accurate pre-positioning of T\u00a0cell and antigen-presenting cell membranes. Comparisons of the ligand-bound and unliganded receptors, along with molecular dynamics simulations, indicate that TCRs can be triggered in the absence of spontaneous structural rearrangements.","bibjson":{"author":[{"initials":"L","lastname":"Su\u0161ac","name":"Su\u0161ac L"},{"initials":"MT","lastname":"Vuong","name":"Vuong MT"},{"initials":"C","lastname":"Thomas","name":"Thomas C"},{"initials":"S","lastname":"von B\u00fclow","name":"von B\u00fclow S"},{"initials":"C","lastname":"O'Brien-Ball","name":"O'Brien-Ball C"},{"initials":"AM","lastname":"Santos","name":"Santos AM"},{"initials":"RA","lastname":"Fernandes","name":"Fernandes RA"},{"initials":"G","lastname":"Hummer","name":"Hummer G"},{"initials":"R","lastname":"Tamp\u00e9","name":"Tamp\u00e9 R"},{"initials":"SJ","lastname":"Davis","name":"Davis SJ"}],"identifier":[{"id":"10.1016/j.cell.2022.07.010","type":"doi"},{"id":"35985289","type":"pubmed"}],"issue":["17"],"journal":{"iso_abbreviation":"Cell","name":""},"pages":["3201-3213.e19"],"title":"Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S0092867422009138","volume":["185"],"year":[2022]},"in_pmc":"N","in_pmce":"N","open_access":"N"},"resolution":"3.08","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/7phr"},"rcsb":{"url":"https://www.rcsb.org/structure/7phr"},"stcrdab":{"url":"http://opig.stats.ox.ac.uk/webapps/stcrdab/StrViewer?pdb=7phr"}},"species":{"common_name":"Human","match_type":"histo:override","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":{"alpha":{"chains":["A"],"subgroup":"TRAV17"},"beta":{"chains":["B"],"subgroup":"TRBV19"},"mhc_type":"class_i","pdb_code":"7phr"},"title":"HLA-A*02:01 presenting \"YLEPGPVTV\" to Alpha/Beta T cell receptor at 3.08&#8491; resolution","unique_chain_count":5}}
