{"display":true,"structure":{"allele":{"alpha":{"identifier":"ipd-imgt:HLA35225","locus":"hla-f","match_type":"histo:exact","name":"HLA-F*01:01","slug":"hla_f_01_01","species_stem":"hla"},"beta":{}},"assemblies":{"1":{"assembly_name":"5knm_1","chains":["A","B","D","N"],"downloaded_at":"2022-11-09T14:37:56.145774"}},"assembly_count":null,"assigned_chains":{"beta2m":{"chains":["B"],"match_type":"histo:assign_chains","score":0.7,"sequence":"MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADLHHHHHHHHGSGGLEVLFQGPEFGGSADPIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGGGGSGGSGSGGGS"},"class_i_alpha":{"chains":["A"],"match_type":"histo:assign_chains","score":0.82,"sequence":"GSHSLRYFSTAVSRPGRGEPRYIAVEYVDDTQFLRFDSDAAIPRMEPREPWVEQEGPQYWEWTTGYAKANAQTDRVALRNLLRRYNQSEAGSHTLQGMNGCDMGPDGRLLRGYHQHAYDGKDYISLNEDLRSWTAADTVAQITQRFYEAEEYAEEFRTYLEGECLELLRRYLENGKETLQRADPPKAHVAHHPISDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPQPLILRWEQSPQPTIPI"},"lir1":{"chains":["D"],"match_type":"histo:assign_chains","score":1.0,"sequence":"MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADLHHHHHHHHGSGGLEVLFQGPEFGGSADLGHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTALWITRIPQELVKKGQFPIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVILQCDSQVAFDGFSLCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNSPYEWSLPSDLLELLVLG"},"peptide":{"chains":["N"],"match_type":"histo:classify_peptide","sequence":"ILRWEQ"}},"chronology":{"deposition_date":"2016-06-28","deposition_year":2016,"release_date":"2017-06-14","release_year":2017,"revision_date":"2020-07-29","revision_year":2020},"class":"class_i","classical":true,"complex_type":"class_i_with_peptide_and_lir1","components":["class_i_alpha","beta2m","peptide","lir1"],"experimental_method":"X-ray diffraction","facets":{},"ligands":[],"locus":"hla-f","manually_edited":{},"missing_residues":[],"page_title":"5KNM | HLA-F*01:01 binding \"ILRWEQ\" with LIR-1 NK receptor","pdb_code":"5knm","pdb_title":"Human Leukocyte Antigen F Presents Peptides and Regulates Immunity through Interactions with NK Cell Receptors.","peptide":{"N":{"actual_length":6,"actual_sequence":"ILRWEQ","chain_id":"N","features":["correct_sequence_and_length","incorrect_start","short_peptide"],"full_length":6,"full_sequence":"ILRWEQ"}},"peptide_length":6,"peptide_length_name":"hexamer","peptide_neighbours":{"2":{"neighbours":[{"position":66,"residue":"TYR"},{"position":62,"residue":"TRP"}],"position":2,"residue":"ILE"},"3":{"neighbours":[{"position":66,"residue":"TYR"},{"position":70,"residue":"ASN"},{"position":69,"residue":"ALA"}],"position":3,"residue":"LEU"},"4":{"neighbours":[{"position":159,"residue":"TYR"},{"position":7,"residue":"TYR"},{"position":66,"residue":"TYR"},{"position":70,"residue":"ASN"},{"position":152,"residue":"TYR"},{"position":156,"residue":"PHE"},{"position":155,"residue":"GLU"},{"position":99,"residue":"ASN"}],"position":4,"residue":"ARG"},"5":{"neighbours":[{"position":8,"residue":"PHE"},{"position":74,"residue":"ASP"},{"position":97,"residue":"GLY"},{"position":116,"residue":"HIS"},{"position":73,"residue":"THR"},{"position":99,"residue":"ASN"},{"position":7,"residue":"TYR"},{"position":66,"residue":"TYR"},{"position":70,"residue":"ASN"},{"position":9,"residue":"SER"},{"position":114,"residue":"HIS"},{"position":152,"residue":"TYR"},{"position":98,"residue":"MET"}],"position":5,"residue":"TRP"},"6":{"neighbours":[{"position":114,"residue":"HIS"},{"position":152,"residue":"TYR"},{"position":147,"residue":"TYR"},{"position":150,"residue":"GLU"}],"position":6,"residue":"GLU"},"7":{"neighbours":[{"position":147,"residue":"TYR"},{"position":114,"residue":"HIS"},{"position":77,"residue":"ALA"},{"position":143,"residue":"THR"},{"position":74,"residue":"ASP"},{"position":116,"residue":"HIS"},{"position":73,"residue":"THR"}],"position":7,"residue":"GLN"}},"peptide_sequence":"ILRWEQ","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":"L","three_letter":"LEU"},"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":"T","three_letter":"THR"},"a66":{"number":66,"one_letter":"Y","three_letter":"TYR"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"}},"b":{"a24":{"number":24,"one_letter":"A","three_letter":"ALA"},"a34":{"number":34,"one_letter":"L","three_letter":"LEU"},"a45":{"number":45,"one_letter":"M","three_letter":"MET"},"a63":{"number":63,"one_letter":"T","three_letter":"THR"},"a66":{"number":66,"one_letter":"Y","three_letter":"TYR"},"a67":{"number":67,"one_letter":"A","three_letter":"ALA"},"a7":{"number":7,"one_letter":"Y","three_letter":"TYR"},"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"a9":{"number":9,"one_letter":"S","three_letter":"SER"},"a99":{"number":99,"one_letter":"N","three_letter":"ASN"}},"c":{"a70":{"number":70,"one_letter":"N","three_letter":"ASN"},"a73":{"number":73,"one_letter":"T","three_letter":"THR"},"a74":{"number":74,"one_letter":"D","three_letter":"ASP"},"a9":{"number":9,"one_letter":"S","three_letter":"SER"},"a97":{"number":97,"one_letter":"G","three_letter":"GLY"}},"d":{"a114":{"number":114,"one_letter":"H","three_letter":"HIS"},"a155":{"number":155,"one_letter":"E","three_letter":"GLU"},"a156":{"number":156,"one_letter":"F","three_letter":"PHE"},"a159":{"number":159,"one_letter":"Y","three_letter":"TYR"},"a160":{"number":160,"one_letter":"L","three_letter":"LEU"},"a99":{"number":99,"one_letter":"N","three_letter":"ASN"}},"e":{"a114":{"number":114,"one_letter":"H","three_letter":"HIS"},"a147":{"number":147,"one_letter":"Y","three_letter":"TYR"},"a152":{"number":152,"one_letter":"Y","three_letter":"TYR"},"a156":{"number":156,"one_letter":"F","three_letter":"PHE"},"a97":{"number":97,"one_letter":"G","three_letter":"GLY"}},"f":{"a116":{"number":116,"one_letter":"H","three_letter":"HIS"},"a123":{"number":123,"one_letter":"Y","three_letter":"TYR"},"a143":{"number":143,"one_letter":"T","three_letter":"THR"},"a146":{"number":146,"one_letter":"F","three_letter":"PHE"},"a147":{"number":147,"one_letter":"Y","three_letter":"TYR"},"a77":{"number":77,"one_letter":"A","three_letter":"ALA"},"a80":{"number":80,"one_letter":"N","three_letter":"ASN"},"a81":{"number":81,"one_letter":"L","three_letter":"LEU"},"a84":{"number":84,"one_letter":"R","three_letter":"ARG"},"a95":{"number":95,"one_letter":"L","three_letter":"LEU"}}},"publication":{"abstract":"Evidence is mounting that the major histocompatibility complex (MHC) molecule HLA-F (human leukocyte antigen\u00a0F) regulates the immune system in pregnancy, infection, and autoimmunity by signaling through NK\u00a0cell receptors (NKRs). We present structural, biochemical, and evolutionary analyses demonstrating that HLA-F presents peptides of unconventional length dictated by a newly arisen mutation (R62W) that has produced an open-ended groove accommodating particularly long peptides. Compared to empty HLA-F open conformers (OCs), HLA-F tetramers bound with human-derived peptides differentially stained leukocytes, suggesting peptide-dependent engagement. Our in\u00a0vitro studies confirm that NKRs differentiate between peptide-bound and peptide-free HLA-F. The complex structure of peptide-loaded \u03b2<sub>2</sub>m-HLA-F bound to the inhibitory LIR1 revealed similarities to high-affinity recognition of the viral MHC-I mimic UL18 and a docking strategy that relies on contacts with HLA-F as well as \u03b2<sub>2</sub>m, thus precluding binding to HLA-F OCs. These findings provide a biochemical framework to understand how HLA-F could regulate immunity via interactions with NKRs.","bibjson":{"author":[{"initials":"CL","lastname":"Dulberger","name":"Dulberger CL"},{"initials":"CP","lastname":"McMurtrey","name":"McMurtrey CP"},{"initials":"A","lastname":"H\u00f6lzemer","name":"H\u00f6lzemer A"},{"initials":"KE","lastname":"Neu","name":"Neu KE"},{"initials":"V","lastname":"Liu","name":"Liu V"},{"initials":"AM","lastname":"Steinbach","name":"Steinbach AM"},{"initials":"WF","lastname":"Garcia-Beltran","name":"Garcia-Beltran WF"},{"initials":"M","lastname":"Sulak","name":"Sulak M"},{"initials":"B","lastname":"Jabri","name":"Jabri B"},{"initials":"VJ","lastname":"Lynch","name":"Lynch VJ"},{"initials":"M","lastname":"Altfeld","name":"Altfeld M"},{"initials":"WH","lastname":"Hildebrand","name":"Hildebrand WH"},{"initials":"EJ","lastname":"Adams","name":"Adams EJ"}],"identifier":[{"id":"10.1016/j.immuni.2017.06.002","type":"doi"},{"id":"28636952","type":"pubmed"}],"issue":["6"],"journal":{"iso_abbreviation":"Immunity","name":""},"pages":["1018-1029.e7"],"title":"Human Leukocyte Antigen F Presents Peptides and Regulates Immunity through Interactions with NK Cell Receptors.","type":"article","url":"https://www.sciencedirect.com/science/article/abs/pii/S1074761317302297","volume":["46"],"year":[2017]},"in_pmc":"N","in_pmce":"Y","open_access":"N"},"resolution":"3.30","same_as":{"pdbe":{"url":"https://www.ebi.ac.uk/pdbe/entry/pdb/5knm"},"rcsb":{"url":"https://www.rcsb.org/structure/5knm"}},"species":{"common_name":"Human","match_type":"histo:assign_species","scientific_name":"Homo sapiens","slug":"homo_sapiens"},"tcr":null,"title":"HLA-F*01:01 binding \"ILRWEQ\" with LIR-1 NK receptor at 3.30&#8491; resolution","unique_chain_count":4}}