{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:43:24Z","timestamp":1791852204126,"version":"4.3.4"},"update-to":[{"DOI":"10.1371\/journal.pbio.3001057","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,5,6]],"date-time":"2021-05-06T00:00:00Z","timestamp":1620259200000}}],"reference-count":82,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T00:00:00Z","timestamp":1619395200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["110106\/Z\/15\/Z"],"award-info":[{"award-number":["110106\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012353","name":"Deutschen Konsortium f\u00fcr Translationale Krebsforschung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012353","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural and Medical Sciences Institute"},{"DOI":"10.13039\/501100001663","name":"Volkswagen Foundation","doi-asserted-by":"publisher","award":["Lichtenberg grant A112662"],"award-info":[{"award-number":["Lichtenberg grant A112662"]}],"id":[{"id":"10.13039\/501100001663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BMBF FugatoPlus","award":["AvImmun"],"award-info":[{"award-number":["AvImmun"]}]},{"name":"ERA Net","award":["ANIHWA-MADISUP"],"award-info":[{"award-number":["ANIHWA-MADISUP"]}]}],"content-domain":{"domain":["www.plosbiology.org"],"crossmark-restriction":false},"short-container-title":["PLoS Biol"],"abstract":"<jats:p>Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek\u2019s disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek\u2019s disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the 2 class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek\u2019s disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only 4 viral genes, nearly all having the peptide motif for BL2*02, the dominantly expressed class II molecule in chickens. We expressed BL2*02 linked to several Marek\u2019s disease virus (MDV) peptides and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to a core binding peptide of 10 amino acids, compared to the 9 amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.<\/jats:p>","DOI":"10.1371\/journal.pbio.3001057","type":"journal-article","created":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T15:48:19Z","timestamp":1619452099000},"page":"e3001057","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":28,"title":["The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek\u2019s disease virus peptides by using an unprecedented binding motif"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4612-5234","authenticated-orcid":true,"given":"Samer","family":"Halabi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5550-9531","authenticated-orcid":true,"given":"Michael","family":"Ghosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1954-7762","authenticated-orcid":true,"given":"Stefan","family":"Stevanovi\u0107","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans-Georg","family":"Rammensee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0698-5395","authenticated-orcid":true,"given":"Luca D.","family":"Bertzbach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1328-2695","authenticated-orcid":true,"given":"Benedikt B.","family":"Kaufer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin C.","family":"Moncrieffe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4447-3251","authenticated-orcid":true,"given":"Bernd","family":"Kaspers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7957-7827","authenticated-orcid":true,"given":"Sonja","family":"H\u00e4rtle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7216-8422","authenticated-orcid":true,"given":"Jim","family":"Kaufman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,4,26]]},"reference":[{"key":"pbio.3001057.ref001","volume-title":"Emerging Viral Diseases: The One Health Connection: Workshop Summary.","author":"Forum on Microbial Threats; Board on Global Health; Institute of Medicine","year":"2015"},{"key":"pbio.3001057.ref002","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1016\/j.puhe.2016.09.018","article-title":"\u2019Between Combat boots and Birkenstocks\u2019-Lessons from HIV\/AIDS, SARS, H1N1 and Ebola.","volume":"141","author":"R Crawford","year":"2016","journal-title":"Public Health."},{"key":"pbio.3001057.ref003","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1111\/imcb.12419","article-title":"COVID-19, varying genetic resistance to viral disease, and immune tolerance checkpoints","volume":"99","author":"CC Goodnow","year":"2021","journal-title":"Immunol Cell Biol"},{"key":"pbio.3001057.ref004","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1146\/annurev-genom-091212-153455","article-title":"Major histocompatibility complex genomics and human disease","volume":"14","author":"J Trowsdale","year":"2013","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"pbio.3001057.ref005","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1146\/annurev-biochem-011520-102754","article-title":"HLAs, TCRs, and KIRs, a triumvirate of human cell-mediated immunity","volume":"89","author":"Z Djaoud","year":"2020","journal-title":"Annu Rev Biochem"},{"key":"pbio.3001057.ref006","doi-asserted-by":"crossref","first-page":"375","DOI":"10.3382\/ps\/pev379","article-title":"Brief review of the chicken Major Histocompatibility Complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance","volume":"95","author":"M Miller","year":"2016","journal-title":"Poult Sci"},{"key":"pbio.3001057.ref007","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.it.2018.01.001","article-title":"Generalists and Specialists: A new view of how MHC class I molecules fight infectious pathogens.","volume":"39","author":"J Kaufman","year":"2018","journal-title":"Trends Immunol"},{"issue":"48","key":"pbio.3001057.ref008","first-page":"417","article-title":"Electron microscope studies of four strains of infectious bronchitis virus","volume":"13","author":"RL Reagan","year":"1952","journal-title":"Am J Vet Res"},{"issue":"9","key":"pbio.3001057.ref009","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1016\/j.tim.2017.06.008","article-title":"Epidemiology, Evolution, and Pathogenesis of H7N9 Influenza Viruses in Five Epidemic Waves since 2013 in China.","volume":"25","author":"S Su","year":"2017","journal-title":"Trends Microbiol."},{"issue":"4","key":"pbio.3001057.ref010","first-page":"1529","article-title":"Knowledge, attitudes, and practices associated with avian influenza along the live chicken market chains in Eastern China: A cross-sectional survey in Shanghai, Anhui, and Jiangsu.","volume":"66","author":"X Zhou","year":"2019","journal-title":"Transbound Emerg Dis."},{"issue":"3\u20134","key":"pbio.3001057.ref011","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.prevetmed.2015.04.013","article-title":"An observational study of the temporal and spatial patterns of Marek\u2019s-disease-associated leukosis condemnation of young chickens in the United States of America","volume":"120","author":"DA Kennedy","year":"2015","journal-title":"Prev Vet Med"},{"key":"pbio.3001057.ref012","first-page":"25","article-title":"Pathogenesis of Marek\u2019s disease virus infection","volume":"255","author":"B. Calnek","year":"2001","journal-title":"Curr Top Microbiol Immunol"},{"key":"pbio.3001057.ref013","first-page":"47","article-title":"Biology of the chicken MHC (B complex).","volume":"12","author":"J Plachy","year":"1992","journal-title":"Crit Rev Immunol."},{"key":"pbio.3001057.ref014","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/nrmicro1382","article-title":"Marek\u2019s disease virus: from miasma to model","volume":"4","author":"N Osterrieder","year":"2006","journal-title":"Nat Rev Microbiol"},{"key":"pbio.3001057.ref015","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.vetmic.2016.11.024","article-title":"Marek\u2019s disease vaccines: Current status, and strategies for improvement and development of vector vaccines","volume":"206","author":"S Reddy","year":"2017","journal-title":"Vet Microbiol"},{"key":"pbio.3001057.ref016","doi-asserted-by":"crossref","first-page":"647","DOI":"10.3390\/cancers12030647","article-title":"Latest Insights into Marek\u2019s disease virus pathogenesis and tumorigenesis.","volume":"12","author":"L Bertzbach","year":"2020","journal-title":"Cancers (Basel)."},{"key":"pbio.3001057.ref017","doi-asserted-by":"crossref","first-page":"149","DOI":"10.2307\/1592455","article-title":"Increased virulence of Marek\u2019s disease virus field isolates","volume":"41","author":"R. Witter","year":"1997","journal-title":"Avian Dis"},{"key":"pbio.3001057.ref018","doi-asserted-by":"crossref","first-page":"e1002198","DOI":"10.1371\/journal.pbio.1002198","article-title":"Imperfect vaccination can enhance the transmission of highly virulent pathogens","volume":"13","author":"A Read","year":"2015","journal-title":"PLoS Biol"},{"key":"pbio.3001057.ref019","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1016\/j.immuni.2007.11.007","article-title":"Structures of an MHC class I molecule from B21 chickens illustrate promiscuous peptide binding","volume":"27","author":"M Koch","year":"2007","journal-title":"Immunity"},{"key":"pbio.3001057.ref020","doi-asserted-by":"crossref","first-page":"e05345","DOI":"10.7554\/eLife.05345","article-title":"Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding","volume":"4","author":"P Chappell","year":"2015","journal-title":"Elife"},{"key":"pbio.3001057.ref021","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1007\/s00251-008-0307-1","article-title":"High allelic polymorphism, moderate sequence diversity and diversifying selection for B-NK but not B-lec, the pair of lectin-like receptor genes in the chicken MHC","volume":"60","author":"S Rogers","year":"2008","journal-title":"Immunogenetics"},{"key":"pbio.3001057.ref022","doi-asserted-by":"crossref","first-page":"16740","DOI":"10.1073\/pnas.0906776106","article-title":"BG1 has a major role in MHC-linked resistance to malignant lymphoma in the chicken","volume":"106","author":"R Goto","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pbio.3001057.ref023","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1007\/s00251-004-0760-4","article-title":"Identification of peptides associated with chicken major histocompatibility complex class II molecules of B21 and B19 haplotypes","volume":"56","author":"M Haeri","year":"2005","journal-title":"Immunogenetics"},{"key":"pbio.3001057.ref024","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1111\/j.1365-2052.2006.01459.x","article-title":"Chicken major histocompatibility complex class II molecules of the B haplotype present self and foreign peptides","volume":"37","author":"J Cumberbatch","year":"2006","journal-title":"Anim Genet"},{"key":"pbio.3001057.ref025","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.virol.2006.09.010","article-title":"Marek\u2019s disease virus up-regulates major histocompatibility complex class II cell surface expression in infected cells","volume":"359","author":"M Niikura","year":"2007","journal-title":"Virology"},{"key":"pbio.3001057.ref026","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.coi.2017.03.013","article-title":"What chickens might tell us about the MHC class II system","volume":"46","author":"A Parker","year":"2017","journal-title":"Curr Opin Immunol"},{"key":"pbio.3001057.ref027","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/368215a0","article-title":"Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide","volume":"368","author":"L Stern","year":"1994","journal-title":"Nature"},{"key":"pbio.3001057.ref028","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1016\/j.molimm.2009.10.008","article-title":"Peptide binding to MHC class I and II proteins: new avenues from new methods","volume":"47","author":"R Yaneva","year":"2010","journal-title":"Mol Immunol"},{"key":"pbio.3001057.ref029","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1016\/j.cell.2012.11.025","article-title":"Crystal structure of the HLA-DM-HLA-DR1 complex defines mechanisms for rapid peptide selection","volume":"151","author":"W Pos","year":"2012","journal-title":"Cell"},{"key":"pbio.3001057.ref030","doi-asserted-by":"crossref","first-page":"5405","DOI":"10.1073\/pnas.1118801109","article-title":"Crystal structure of a complete ternary complex of T-cell receptor, peptide-MHC, and CD4","volume":"109","author":"Y Yin","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pbio.3001057.ref031","doi-asserted-by":"crossref","first-page":"4950","DOI":"10.1073\/pnas.1102524108","article-title":"Essential glycan-dependent interactions optimize MHC class I peptide loading","volume":"108","author":"P Wearsch","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pbio.3001057.ref032","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/42523","article-title":"Crystal structure of the complex between human CD8alpha(alpha) and HLA-A2.","volume":"387","author":"G Gao","year":"1997","journal-title":"Nature"},{"key":"pbio.3001057.ref033","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1007\/s00251-003-0620-7","article-title":"The properties of the single chicken MHC classical class II alpha chain (B-LA) gene indicate an ancient origin for the DR\/E-like isotype of class II molecules.","volume":"55","author":"J Salomonsen","year":"2003","journal-title":"Immunogenetics"},{"key":"pbio.3001057.ref034","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1007\/s002510050369","article-title":"Class II MHC cDNAs in 15I5 B-congenic chickens.","volume":"47","author":"G Pharr","year":"1998","journal-title":"Immunogenetics"},{"key":"pbio.3001057.ref035","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1007\/s002510050022","article-title":"The major and a minor class II beta-chain (B-LB) gene flank the tapasin gene in the B-F \/B-L region of the chicken major histocompatibility complex.","volume":"51","author":"J Jacob","year":"2000","journal-title":"Immunogenetics"},{"key":"pbio.3001057.ref036","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1089\/vim.2009.0047","article-title":"Early replication in pulmonary B cells after infection with Marek\u2019s disease herpesvirus by the respiratory route","volume":"22","author":"BJ Baaten","year":"2009","journal-title":"Viral Immunol"},{"key":"pbio.3001057.ref037","doi-asserted-by":"crossref","first-page":"7279","DOI":"10.1073\/pnas.1424420112","article-title":"In vitro model for lytic replication, latency, and transformation of an oncogenic alphaherpesvirus","volume":"112","author":"J Schermuly","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pbio.3001057.ref038","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1007\/978-1-4939-9450-2_10","article-title":"Purification and identification of naturally presented MHC class I and II ligands","volume":"1988","author":"A Nelde","year":"2019","journal-title":"Methods Mol Biol"},{"key":"pbio.3001057.ref039","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.1038\/s41596-019-0133-y","article-title":"Mass spectrometry-based identification of MHC-bound peptides for immunopeptidomics","volume":"14","author":"A Purcell","year":"2019","journal-title":"Nat Protoc"},{"key":"pbio.3001057.ref040","first-page":"789","article-title":"Nature of genetic resistance to Marek\u2019s disease in chickens","volume":"66","author":"L Lee","year":"1981","journal-title":"J Natl Cancer Inst"},{"key":"pbio.3001057.ref041","doi-asserted-by":"crossref","first-page":"259","DOI":"10.3382\/ps.0602559","article-title":"Influence of oncogenicity of Marek\u2019s disease virus on evaluation of genetic resistance","volume":"60","author":"K Schat","year":"1981","journal-title":"Poult Sci"},{"key":"pbio.3001057.ref042","doi-asserted-by":"crossref","first-page":"108","DOI":"10.2307\/1588905","article-title":"Control of Marek\u2019s disease in the Netherlands. I. Isolation of an avirulent Marek\u2019s disease virus (strain CVI 988) and its use in laboratory vaccination trials.","volume":"16","author":"B Rispens","year":"1972","journal-title":"Avian Dis"},{"key":"pbio.3001057.ref043","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1007\/BF00211553","article-title":"Organization of a functional chicken class II B gene","volume":"31","author":"R Zoorob","year":"1990","journal-title":"Immunogenetics"},{"key":"pbio.3001057.ref044","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.4049\/jimmunol.1901305","article-title":"A newly recognized pairing mechanism of the \u03b1- and \u03b2-chains of the chicken peptide-MHC class II complex","volume":"204","author":"L Zhang","year":"2020","journal-title":"J Immunol"},{"key":"pbio.3001057.ref045","doi-asserted-by":"crossref","first-page":"9","DOI":"10.2307\/1588081","article-title":"Studies on genetic resistance to Marek\u2019s disease","volume":"12","author":"R. Cole","year":"1968","journal-title":"Avian Dis"},{"key":"pbio.3001057.ref046","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1006\/smim.1994.1050","article-title":"Evolutionary conservation of MHC class I and class II molecules\u2014different yet the same","volume":"6","author":"J Kaufman","year":"1994","journal-title":"Semin Immunol"},{"key":"pbio.3001057.ref047","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.4049\/jimmunol.1800611","article-title":"An invariant arginine in common with MHC Class II allows extension at the C-terminal end of peptides bound to chicken MHC class I","volume":"201","author":"J Xiao","year":"2018","journal-title":"J Immunol"},{"key":"pbio.3001057.ref048","doi-asserted-by":"crossref","first-page":"13279","DOI":"10.1073\/pnas.0403371101","article-title":"A hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition","volume":"101","author":"Z Zavala-Ruiz","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pbio.3001057.ref049","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1016\/j.chembiol.2004.08.007","article-title":"A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins","volume":"11","author":"Z Zavala-Ruiz","year":"2004","journal-title":"Chem Biol"},{"key":"pbio.3001057.ref050","doi-asserted-by":"crossref","first-page":"264","DOI":"10.3390\/v11030264","article-title":"The transcriptional landscape of Marek\u2019s disease virus in primary chicken B cells reveals novel splice variants and genes.","volume":"11","author":"L Bertzbach","year":"2019","journal-title":"Viruses"},{"key":"pbio.3001057.ref051","doi-asserted-by":"crossref","first-page":"92","DOI":"10.4049\/jimmunol.1100590","article-title":"Cytotoxic CD4+ T cell responses to EBV contrast with CD8 responses in breadth of lytic cycle antigen choice and in lytic cycle recognition","volume":"187","author":"H Long","year":"2011","journal-title":"J Immunol"},{"key":"pbio.3001057.ref052","doi-asserted-by":"crossref","first-page":"5827","DOI":"10.4049\/jimmunol.1302060","article-title":"CD4 T cells specific for a latency-associated \u03b3-herpesvirus epitope are polyfunctional and cytotoxic","volume":"193","author":"M Freeman","year":"2014","journal-title":"J Immunol"},{"key":"pbio.3001057.ref053","doi-asserted-by":"crossref","first-page":"4776","DOI":"10.1128\/JVI.06573-11","article-title":"Human CD4+ T cell response to human herpesvirus 6","volume":"86","author":"M Nastke","year":"2012","journal-title":"J Virol"},{"key":"pbio.3001057.ref054","doi-asserted-by":"crossref","first-page":"6814","DOI":"10.4049\/jimmunol.178.11.6814","article-title":"Vaccinia virus-specific CD4+ T cell responses target a set of antigens largely distinct from those targeted by CD8+ T cell responses","volume":"78","author":"M Moutaftsi","year":"2007","journal-title":"J Immunol"},{"key":"pbio.3001057.ref055","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1371\/journal.ppat.0030144","article-title":"Human CD4+ T cell epitopes from vaccinia virus induced by vaccination or infection","volume":"3","author":"J Calvo-Calle","year":"2007","journal-title":"PLoS Pathog"},{"key":"pbio.3001057.ref056","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1002\/eji.1830230219","article-title":"The set of naturally processed peptides displayed by DR molecules is tuned by polymorphism of residue 86","volume":"23","author":"S Demotz","year":"1993","journal-title":"Eur J Immunol"},{"key":"pbio.3001057.ref057","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1111\/j.1399-0039.1985.tb00450.x","article-title":"Analysis of chickens for recombination within the MHC (B-complex).","volume":"25","author":"K Skj\u00f8dt","year":"1985","journal-title":"Tissue Antigens"},{"key":"pbio.3001057.ref058","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1007\/BF00355375","article-title":"Attempt to detect recombination between B-F and B-L genes within the chicken B complex by serological typing, in vitro MLR, and RFLP analyses","volume":"28","author":"K H\u00e1la","year":"1988","journal-title":"Immunogenetics"},{"key":"pbio.3001057.ref059","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12711-015-0181-x","article-title":"A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1","volume":"48","author":"J Fulton","year":"2016","journal-title":"Genet Sel Evol"},{"key":"pbio.3001057.ref060","doi-asserted-by":"crossref","first-page":"588","DOI":"10.3390\/microorganisms7120588","article-title":"Marek\u2019s disease virus infection of natural killer cells.","volume":"7","author":"L Bertzbach","year":"2019","journal-title":"Microorganisms"},{"key":"pbio.3001057.ref061","volume-title":"\u201cCell-culture Methods\u201d In A laboratory manual for the isolation and identification of avian pathogens.","author":"K Schat","year":"1998","edition":"4"},{"key":"pbio.3001057.ref062","doi-asserted-by":"crossref","first-page":"345","DOI":"10.2307\/1591417","article-title":"Transfection of chicken embryo fibroblasts with Marek\u2019s disease virus DNA","volume":"34","author":"RW Morgan","year":"1990","journal-title":"Avian Dis"},{"key":"pbio.3001057.ref063","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1093\/intimm\/dxl137","article-title":"Unique and conserved functions of B cell-activating factor of the TNF family (BAFF) in the chicken.","volume":"19","author":"S Kothlow","year":"2007","journal-title":"Int Immunol"},{"key":"pbio.3001057.ref064","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/j.dci.2004.09.001","article-title":"Conservation of biological properties of the CD40 ligand, CD154, in a non-mammalian vertebrate","volume":"29","author":"CA Tregaskes","year":"2005","journal-title":"Dev Comp Immunol"},{"key":"pbio.3001057.ref065","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/351290a0","article-title":"Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules","volume":"351","author":"K Falk","year":"1991","journal-title":"Nature"},{"key":"pbio.3001057.ref066","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/BF00364870","article-title":"Mouse monoclonal antibodies to class I and class II antigens of the chicken MHC","volume":"21","author":"M Crone","year":"1985","journal-title":"Immunogenetics"},{"key":"pbio.3001057.ref067","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1074\/mcp.C119.001652","article-title":"Guidance Document: validation of a high-performance liquid chromatography-tandem mass spectrometry immunopeptidomics assay for the identification of HLA class I ligands suitable for pharmaceutical therapies","volume":"19","author":"A Ghosh","year":"2020","journal-title":"Molec Cell Proteomics."},{"key":"pbio.3001057.ref068","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1038\/nmeth1113","article-title":"Semi-supervised learning for peptide identification from shotgun proteomics datasets","volume":"4","author":"L Kall","year":"2007","journal-title":"Nat Methods"},{"issue":"D1","key":"pbio.3001057.ref069","doi-asserted-by":"crossref","first-page":"D442","DOI":"10.1093\/nar\/gky1106","article-title":"The PRIDE database and related tools and resources in 2019: improving support for quantification data","volume":"47","author":"Y Perez-Riverol","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pbio.3001057.ref070","doi-asserted-by":"crossref","first-page":"W458","DOI":"10.1093\/nar\/gkx248","article-title":"GibbsCluster: unsupervised clustering and alignment of peptide sequences","volume":"45","author":"M Andreatta","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pbio.3001057.ref071","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1186\/1471-2164-9-488","article-title":"BioVenn\u2014a web appliaction for the comparison and visualization of biological lists usnig area-proportional Venn diagrams","volume":"9","author":"T Hulsen","year":"2008","journal-title":"BMC Genomics"},{"key":"pbio.3001057.ref072","first-page":"20156","article-title":"Expression of recomginant HLA-DR2 molecules. Replacement of the hydrophobic transmembrane region by a leucine zipper dimerization motif allows the assembly and secretion of soluble DR alpha beta heterodimers","volume":"271","author":"A Kalandadze","year":"1996","journal-title":"J Biol Chem"},{"key":"pbio.3001057.ref073","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1107\/S0907444909047337","article-title":"XDS","volume":"66","author":"W. Kabsch","year":"2010","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"pbio.3001057.ref074","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1107\/S0907444913000061","article-title":"How good are my data and what is the resolution?","volume":"69","author":"PR Evans","year":"2013","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"pbio.3001057.ref075","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1107\/S0907444910045749","article-title":"Overview of the CCP4 suite and current developments","volume":"67","author":"MD Winn","year":"2011","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"pbio.3001057.ref076","doi-asserted-by":"crossref","first-page":"13224","DOI":"10.1038\/ncomms13224","article-title":"MHC class II complexes sample intermediate states along the peptide exchange pathway","volume":"7","author":"M Wieczorek","year":"2016","journal-title":"Nat Commun"},{"key":"pbio.3001057.ref077","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"P Emsley","year":"2010","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"Pt 2","key":"pbio.3001057.ref078","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S0907444909052925","article-title":"PHENIX: a comprehensive Python-based system for macromolecular structure solution","volume":"66","author":"PD Adams","year":"2010","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"pbio.3001057.ref079","doi-asserted-by":"crossref","first-page":"2778","DOI":"10.1021\/ci200227u","article-title":"LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.","volume":"51","author":"RA Laskowski","year":"2011","journal-title":"J Chem Inf Model"},{"key":"pbio.3001057.ref080","doi-asserted-by":"crossref","first-page":"2743","DOI":"10.1016\/j.molimm.2008.02.017","article-title":"Reshuffling of ancient peptide binding motifs between HLA-DRB multigene family members: old wine served in new skins","volume":"45","author":"GG Doxiadis","year":"2008","journal-title":"Mol Immunol"},{"key":"pbio.3001057.ref081","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1021\/bi00270a027","article-title":"N-terminal amino acid sequences of the \u03b1 and \u03b2 chains of HLA-DR and HLA-DR2 antigens","volume":"22","author":"LE Walker","year":"1983","journal-title":"Biochemistry"},{"key":"pbio.3001057.ref082","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0092-8674(84)90068-0","article-title":"The class II molecules of the human and murine major histocompatibility complex","volume":"36","author":"JF Kaufman","year":"1984","journal-title":"Cell"}],"updated-by":[{"DOI":"10.1371\/journal.pbio.3001057","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,5,6]],"date-time":"2021-05-06T00:00:00Z","timestamp":1620259200000}}],"container-title":["PLOS Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3001057","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T11:42:43Z","timestamp":1620733363000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3001057"}},"subtitle":[],"editor":[{"given":"Philippa","family":"Marrack","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,4,26]]},"references-count":82,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2021,4,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pbio.3001057","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.11.27.400937","asserted-by":"object"}]},"ISSN":["1545-7885"],"issn-type":[{"value":"1545-7885","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,26]]}}}