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Here we demonstrate that diverse H5 HAs can use MHC-II to enter cells, with avian MHC-II enabling more efficient entry than human MHC-II for most H5 HAs. To define the molecular interface, we use pseudovirus deep mutational scanning to measure how mutations to H5 HA affect its interaction with tufted duck MHC-II, and identify mutations that restrict HA to exclusively MHC-II or sialic acid receptors. We leverage identification of H5 HA mutations that increase binding to tufted duck MHC-II to determine a 4.8 \u00c5 cryo-EM model of the complex. To support the structural model, we measure how all mutations to tufted duck MHC-II affect its interaction with H5 HA, and find the alpha chain is the dominant determinant but beta chain sites near the peptide-binding groove also contribute. To generalize these findings, we use deep mutational scanning to show that a H7 HA interacts with MHC-II similarly to H5 HA. Finally, we show that H1, H2, H3, and H9 HAs interact with avian or human MHC-II, although interactions vary among strains that evolved in different hosts.<\/jats:p>","DOI":"10.64898\/2026.07.17.738765","type":"posted-content","created":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T20:50:12Z","timestamp":1784753412000},"source":"Crossref","is-referenced-by-count":0,"title":["Defining the molecular interaction between influenza hemagglutinin and MHC-II"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0908-6982","authenticated-orcid":false,"given":"Bernadeta","family":"Dadonaite","sequence":"first","affiliation":[{"name":"Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annie","family":"Dosey","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington, Seattle, WA 98195, USA"},{"name":"Institute for Protein Design, University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3912-7162","authenticated-orcid":false,"given":"Jenny J.","family":"Ahn","sequence":"additional","affiliation":[{"name":"Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9972-038X","authenticated-orcid":false,"given":"Timothy C.","family":"Yu","sequence":"additional","affiliation":[{"name":"Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1897-5063","authenticated-orcid":false,"given":"Sara A.","family":"Sunshine","sequence":"additional","affiliation":[{"name":"Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1389-0992","authenticated-orcid":false,"given":"Ariana G.","family":"Farrell","sequence":"additional","affiliation":[{"name":"Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2978-4692","authenticated-orcid":false,"given":"Neil P.","family":"King","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Washington, Seattle, WA 98195, USA"},{"name":"Institute for Protein Design, University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1267-3408","authenticated-orcid":false,"given":"Jesse D.","family":"Bloom","sequence":"additional","affiliation":[{"name":"Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, 98109, USA"},{"name":"Howard Hughes Medical Institute, Seattle, WA, 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072706211700000_2026.07.17.738765v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/440435a"},{"key":"2026072706211700000_2026.07.17.738765v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(83)90150-2"},{"key":"2026072706211700000_2026.07.17.738765v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2024.05.018"},{"key":"2026072706211700000_2026.07.17.738765v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-0955-3"},{"key":"2026072706211700000_2026.07.17.738765v1.5","doi-asserted-by":"crossref","first-page":"2626","DOI":"10.1038\/s41564-024-01771-1","article-title":"MHC class II proteins mediate sialic acid independent entry of human and avian H2N2 influenza A viruses","volume":"9","year":"2024","journal-title":"Nat. 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