{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T16:06:53Z","timestamp":1788970013055,"version":"build-2803163510"},"reference-count":89,"publisher":"National Academy of Sciences","issue":"24","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":183,"URL":"https:\/\/www.pnas.org\/site\/aboutpnas\/licenses.xhtml"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["16-15-00149"],"award-info":[{"award-number":["16-15-00149"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002261","name":"Russian Foundation for Basic Research","doi-asserted-by":"publisher","award":["19-015-00082"],"award-info":[{"award-number":["19-015-00082"]}],"id":[{"id":"10.13039\/501100002261","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2020,6,16]]},"abstract":"<jats:p>\n                    T cell maturation and activation depend upon T cell receptor (TCR) interactions with a wide variety of antigenic peptides displayed in a given major histocompatibility complex (MHC) context. Complementarity-determining region 3 (CDR3) is the most variable part of the TCR\u03b1 and -\u03b2 chains, which govern interactions with peptide\u2013MHC complexes. However, it remains unclear how the CDR3 landscape is shaped by individual MHC context during thymic selection of na\u00efve T cells. We established two mouse strains carrying distinct allelic variants of\n                    <jats:italic>H2-A<\/jats:italic>\n                    and analyzed thymic and peripheral production and TCR repertoires of na\u00efve conventional CD4\n                    <jats:sup>+<\/jats:sup>\n                    T (T\n                    <jats:sub>conv<\/jats:sub>\n                    ) and na\u00efve regulatory CD4\n                    <jats:sup>+<\/jats:sup>\n                    T (T\n                    <jats:sub>reg<\/jats:sub>\n                    ) cells. Compared with tuberculosis-resistant C57BL\/6 (H2-A\n                    <jats:sup>b<\/jats:sup>\n                    ) mice, the tuberculosis-susceptible H2-A\n                    <jats:sup>j<\/jats:sup>\n                    mice had fewer CD4\n                    <jats:sup>+<\/jats:sup>\n                    T cells of both subsets in the thymus. In the periphery, this deficiency was only apparent for T\n                    <jats:sub>conv<\/jats:sub>\n                    and was compensated for by peripheral reconstitution for T\n                    <jats:sub>reg<\/jats:sub>\n                    . We show that H2-A\n                    <jats:sup>j<\/jats:sup>\n                    favors selection of a narrower and more convergent repertoire with more hydrophobic and strongly interacting amino acid residues in the middle of CDR3\u03b1 and CDR3\u03b2, suggesting more stringent selection against a narrower peptide\u2013MHC-II context. H2-A\n                    <jats:sup>j<\/jats:sup>\n                    and H2-A\n                    <jats:sup>b<\/jats:sup>\n                    mice have prominent reciprocal differences in CDR3\u03b1 and CDR3\u03b2 features, probably reflecting distinct modes of TCR fitting to MHC-II variants. These data reveal the mechanics and extent of how MHC-II shapes the na\u00efve CD4\n                    <jats:sup>+<\/jats:sup>\n                    T cell CDR3 landscape, which essentially defines adaptive response to infections and self-antigens.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2003170117","type":"journal-article","created":{"date-parts":[[2020,6,1]],"date-time":"2020-06-01T20:31:01Z","timestamp":1591043461000},"page":"13659-13669","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":55,"title":["MHC-II alleles shape the CDR3 repertoires of conventional and regulatory na\u00efve CD4\n                    <sup>+<\/sup>\n                    T cells"],"prefix":"10.1073","volume":"117","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7086-6158","authenticated-orcid":false,"given":"Nadezhda N.","family":"Logunova","sequence":"first","affiliation":[{"name":"Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, 107564, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeriia V.","family":"Kriukova","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"},{"name":"Center of Life Sciences, Skoltech, Moscow, 143026, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel V.","family":"Shelyakin","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6495-7173","authenticated-orcid":false,"given":"Evgeny S.","family":"Egorov","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"},{"name":"Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alina","family":"Pereverzeva","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2164-5698","authenticated-orcid":false,"given":"Nina G.","family":"Bozhanova","sequence":"additional","affiliation":[{"name":"Center for Structural Biology, Vanderbilt University, Nashville, TN 37235;"},{"name":"Department of Chemistry, Vanderbilt University, Nashville, TN 37235;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7826-7942","authenticated-orcid":false,"given":"Mikhail","family":"Shugay","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"},{"name":"Center of Life Sciences, Skoltech, Moscow, 143026, Russia;"},{"name":"Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitrii S.","family":"Shcherbinin","sequence":"additional","affiliation":[{"name":"Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail V.","family":"Pogorelyy","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"},{"name":"Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina M.","family":"Merzlyak","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"},{"name":"Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasiliy N.","family":"Zubov","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens","family":"Meiler","sequence":"additional","affiliation":[{"name":"Center for Structural Biology, Vanderbilt University, Nashville, TN 37235;"},{"name":"Department of Chemistry, Vanderbilt University, Nashville, TN 37235;"},{"name":"Institute for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0430-790X","authenticated-orcid":false,"given":"Dmitriy M.","family":"Chudakov","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia;"},{"name":"Center of Life Sciences, Skoltech, Moscow, 143026, Russia;"},{"name":"Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, 117997, 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