Trypanosoma brucei is a parasitic protozoan that causes African sleeping sickness. It contains a flagellum required for locomotion and viability. In addition to a microtubular axoneme, the flagellum contains a crystalline paraflagellar rod (PFR) and connecting proteins. We show here, by cryoelectron tomography, the structure of the flagellum in three bending states. The PFR lattice in straight flagella repeats every 56 nm along the length of the axoneme, matching the spacing of the connecting proteins. During flagellar bending, the PFR crystallographic unit cell lengths remain constant while the interaxial angles vary, similar to a jackscrew. The axoneme drives the expansion and compression of the PFR lattice. We propose that the PFR modifies the in-plane axoneme motion to produce the characteristic trypanosome bihelical motility as captured by high-speed light microscope videography.T rypanosoma brucei has devastated the African continent for centuries by infecting humans and domestic animals and has hindered economic development in sub-Saharan Africa (1). Current sleeping sickness treatments are inadequate and the drugs used are highly toxic (2). In recent years, the motility of the T. brucei flagellum has been found to be essential for parasite survival, infection, and disease pathogenesis (3), and has emerged as a promising drug target (4). Flagella with similar structural organization and protein composition have also been found in euglenoids (5) and other kinetoplastid parasites including Leishmania spp. and Trypanosoma cruzi, which cause Leishmaniasis and Chagas disease, respectively (6).The trypanosome flagellum is more complex than most other eukaryotic microtubule-based flagella (7-9) and is completely different from rotary-motor based bacterial flagella (10). Each T. brucei cell contains one flagellum that moves the cell body in an alternating right and left-handed twist resulting in bihelical motion (11) (Movie S1). The membrane-enclosed flagellum, composed of an axoneme, a paraflagellar rod (PFR) (12), and connecting proteins, is attached to the cell body (Fig. 1). PFR was identified as a lattice-like ultrastructure in T. brucei flagellum (13). This periodic and crystalline nature of the PFR was confirmed in T. brucei (14) and related species (15, 16). Monoclonal antibody screens (17) and proteomics studies (18-20) have identified at least 40 PFR proteins. Among them, PFR1 (73 kDa) and PFR2 (69 kDa), containing coiled-coil regions (21), are major structural components of the PFR (22). Depletion of these proteins results in failure of PFR assembly and cell motility defects (17, 23) ( Fig. S1 and Movie S2). In the T. brucei pathogenic bloodstream form, ablation of PFR2 causes death of the parasite (18). These results demonstrate a critical role of the PFR in T. brucei motility and viability. We have employed cryoelectron tomography (cryo-ET) to determine the structure of a biochemically isolated T. brucei flagella (18). We describe here a model that explains how the structure and arrangement of the fl...