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Abstract

Cilia and flagella play very important roles in eukaryotic cells, ranging from cell motility to chemo- and mechanosensation with active involvement in embryonic development and control of cell division. Cilia and flagella are highly dynamic organelles undergoing constant turnover at their tip, where multiprotein precursors synthesized in the cell cytoplasm are assembled, turnover products are released and carried back for recycling. Such bidirectional trafficking is maintained by an ATP-dependent active transport that is carried out by intraflagellar transport (IFT) particles. Despite our knowledge of the cell biology, the genomic, and the biochemistry of IFT, high-resolution 3D models for IFT are still missing. To date, the only information on the 3D structure of IFT come from our analysis of full-length flagella from the biflagellate green alga Chlamydomonas reinhardtii: the model organism where IFT was discovered and first characterized. In this chapter, we describe and discuss the strategy we implemented to produce the first 3D models of in situ IFT trains in flat-embedded flagella. We provide detailed information about the acquisition of tomographic images, the simultaneous alignment of the double-tilt tomographic series, and the analysis of the tomograms by subtomogram averaging for the generation of detailed 3D models of IFT particles.