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While the axonemal structure of motile cilia has been described extensively in recent years, the molecular architecture of the transition zone, basal body, and surrounding ciliary environment of MCCs remain more elusive. Here, we use cryo-focused ion beam (cryo-FIB) milling and cryo-electron tomography (cryo-ET) to obtain\n                  <jats:italic>in situ<\/jats:italic>\n                  3D views of the ciliary base within intact MCCs from mammalian trachea, complemented by\n                  <jats:italic>in situ<\/jats:italic>\n                  cross-linking mass spectrometry (XL\/MS) and ultrastructure expansion microscopy (U-ExM) for molecular identification. Our data reveal spatially-defined modifications of microtubule architecture from the proximal centriole to the early axoneme, including transition zone-specific features such as an A-B linker bridging microtubule doublets and a helical assembly of microtubule inner proteins (MIPs). We show that the ciliary necklace, a feature observed in many motile cilia, is spatially aligned with the transition zone and quantify its regular organization within the membrane. Our\n                  <jats:italic>in situ<\/jats:italic>\n                  data capture rarely observed events, including intraflagellar transport (IFT) trains connecting to ciliary vesicles tethered to undocked centrioles. The surrounding ciliary environment contains intermediate filaments that encircle the basal bodies and bundled actin filaments that elaborate microvilli structures between the cilia. Integration of XL\/MS and U-ExM identified novel microtubule associated proteins (MAPs), MIPs, and membrane-associated proteins localized to these distinct subdomains. This work provides a molecular and structural map of the mammalian MCC ciliary base, revealing architectural principles that underlie its assembly, organization, and function.\n                <\/jats:p>","DOI":"10.64898\/2026.04.05.716577","type":"posted-content","created":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T09:35:11Z","timestamp":1775554511000},"source":"Crossref","is-referenced-by-count":1,"title":["Molecular architecture of the ciliary base in mammalian multiciliated cells"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0872-4527","authenticated-orcid":false,"given":"Caitlyn L.","family":"McCafferty","sequence":"first","affiliation":[{"name":"Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7878-3832","authenticated-orcid":false,"given":"Marine","family":"Brunet","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, University of Geneva, Sciences III, Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4978-8516","authenticated-orcid":false,"given":"Hugo","family":"van den Hoek","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garrison","family":"Buss","sequence":"additional","affiliation":[{"name":"Department of Biology, Stanford University, Stanford, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Mercey","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, University of Geneva, Sciences III, Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8746-1222","authenticated-orcid":false,"given":"Philippe","family":"Van der Stappen","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danilo","family":"Ritz","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4247-4303","authenticated-orcid":false,"given":"Ricardo","family":"Righetto","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0363-1049","authenticated-orcid":false,"given":"Paul","family":"Guichard","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, University of Geneva, Sciences III, Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5092-2343","authenticated-orcid":false,"given":"Virginie","family":"Hamel","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, University of Geneva, Sciences III, Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Stearns","sequence":"additional","affiliation":[{"name":"Department of Biology, Stanford University, Stanford, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0941-4387","authenticated-orcid":false,"given":"Benjamin D.","family":"Engel","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026040900450890000_2026.04.05.716577v1.1","doi-asserted-by":"crossref","unstructured":"Ishikawa, T . 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