PT - JOURNAL ARTICLE AU - Hugo van den Hoek AU - Nikolai Klena AU - Mareike A. Jordan AU - Gonzalo Alvarez Viar AU - Miroslava Schaffer AU - Philipp S. Erdmann AU - William Wan AU - Jürgen M. Plitzko AU - Wolfgang Baumeister AU - Gaia Pigino AU - Virginie Hamel AU - Paul Guichard AU - Benjamin D. Engel TI - <em>In situ</em> architecture of the ciliary base reveals the stepwise assembly of IFT trains AID - 10.1101/2021.10.17.464685 DP - 2021 Jan 01 TA - bioRxiv PG - 2021.10.17.464685 4099 - http://biorxiv.org/content/early/2021/10/17/2021.10.17.464685.short 4100 - http://biorxiv.org/content/early/2021/10/17/2021.10.17.464685.full AB - The cilium is an antenna-like organelle that performs numerous cellular functions, including motility, sensing, and signaling. The base of the cilium contains a selective barrier that regulates the entry of large intraflagellar transport (IFT) trains, which carry cargo proteins required for ciliary assembly and maintenance. However, the native architecture of the ciliary base and the process of IFT train assembly remain unresolved. Here, we use in situ cryo-electron tomography to reveal native structures of the transition zone region and assembling IFT trains at the ciliary base. We combine this direct cellular visualization with ultrastructure expansion microscopy to describe the front-to-back stepwise assembly of IFT trains: IFT-B forms the backbone, onto which IFT-A, then dynein-1b, and finally kinesin-2 sequentially bind before entry into the cilium.Highlight Native molecular structure of the ciliary transition zone and hierarchical order of IFT assembly visualized within Chlamydomonas cells.Competing Interest StatementThe authors have declared no competing interest.