Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Torque transmission mechanism of the curved bacterial flagellar hook revealed by cryo-EM


Bacterial locomotion by rotating flagella is achieved through the hook, which transmits torque from the motor to the filament. The hook is a tubular structure composed of a single type of protein, yet it adopts a curved shape. To perform its function, it must be simultaneously flexible and torsionally rigid. The molecular mechanism by which chemically identical subunits form such a dynamic structure is unknown. Here, we show the complete structure of the hook from Salmonella enterica in its supercoiled ‘curved’ state, at 2.9 Å resolution. Subunits in the curved hook are grouped into 11 distinctive conformations, each shared along 11 protofilaments. The domains of the elongated hook subunit behave as rigid bodies connected by two hinge regions. The reconstituted model demonstrates how identical subunits can dynamically change conformation by physical interactions while bending. These multiple subunit states contradict the two-state model, which is a key feature of flagellar polymorphism.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Cryo-EM of polyhooks from Salmonella enterica.
Fig. 2: Domain motions of subunits around helical turns.
Fig. 3: Subunit interactions in the curved hook.

Data availability

The cryo-EM map of the curved hook has been deposited in the Electron Microscopy Data Bank under accession no. EMD-9909. The atomic coordinates of all 66 subunit models have been deposited in the wwPDB as a single file in mmCIF format under accession no. 6K3I. Source data for Fig. 2c are available with the online version of this paper.


  1. World Health Organization WHO Estimates of the Global Burden of Foodborne Diseases : Foodborne Disease Burden Epidemiology Reference Group 2007–2015 (World Health Organization, 2015).

  2. Fischer Walker, C. L., Perin, J., Aryee, M. J., Boschi-Pinto, C. & Black, R. E. Diarrhea incidence in low- and middle-income countries in 1990 and 2010: a systematic review. BMC Public Health 12, 220 (2012).

    Article  Google Scholar 

  3. Hoffmann, S., Batz, M. B. & Morris, J. G. Annual cost of illness and quality-adjusted life year losses in the United States due to 14 foodborne pathogens. J. Food Prot. 75, 1292–1302 (2012).

    Article  Google Scholar 

  4. Aizawa, S. I. The Flagellar World: Electron Microscopic Images of Bacterial Flagella and Related Surface Structures from More than 30 Species (Academic Press, 2014);

  5. Aizawa, S.-I. Flagellar assembly in Salmonella typhimurium. Mol. Microbiol. 19, 1–5 (1996).

    CAS  Article  Google Scholar 

  6. Fujii, M., Shibata, S. & Aizawa, S.-I. Polar, peritrichous, and lateral flagella belong to three distinguishable flagellar families. J. Mol. Biol. 379, 273–283 (2008).

    CAS  Article  Google Scholar 

  7. Kamiya, R. & Asakura, S. Helical transformations of Salmonella flagella in vitro. J. Mol. Biol. 106, 167–186 (1976).

    CAS  Article  Google Scholar 

  8. Shimada, K., Kamiya, R. & Asakura, S. Left-handed to right-handed helix conversion in Salmonella flagella. Nature 254, 332–334 (1975).

    CAS  Article  Google Scholar 

  9. Kamiya, R., Asakura, S. & Yamaguchi, S. Formation of helical filaments by copolymerization of two types of ‘straight’ flagellins. Nature 286, 628–630 (1980).

    CAS  Article  Google Scholar 

  10. Asakura, S. Polymerization of flagellin and polymorphism of flagella. Adv. Biophys. 1, 99–155 (1970).

    CAS  PubMed  Google Scholar 

  11. Monod, J., Wyman, J. & Changeux, J. P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88–118 (1965).

    CAS  Article  Google Scholar 

  12. Changeux, J.-P. Allostery and the Monod–Wyman–Changeux model after 50 years. Annu. Rev. Biophys. 41, 103–133 (2012).

    CAS  Article  Google Scholar 

  13. Calladine, C. R. Construction of bacterial flagella. Nature 255, 121–124 (1975).

    CAS  Article  Google Scholar 

  14. Kato, S., Okamoto, M. & Asakura, S. Polymorphic transition of the flagellar polyhook from Escherichia coli and Salmonella typhimurium. J. Mol. Biol. 173, 463–476 (1984).

    CAS  Article  Google Scholar 

  15. Egelman, E. H. The iterative helical real space reconstruction method: surmounting the problems posed by real polymers. J. Struct. Biol. 157, 83–94 (2007).

    CAS  Article  Google Scholar 

  16. Williams, A. W. et al. Mutations in fliK and flhB affecting flagellar hook and filament assembly in Salmonella typhimurium. J. Bacteriol. 178, 2960–2970 (1996).

    CAS  Article  Google Scholar 

  17. Barker, C. S., Meshcheryakova, I. V., Kostyukova, A. S., Freddolino, P. L. & Samatey, F. A. An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook. BMC Biol. 15, 97 (2017).

    Article  Google Scholar 

  18. Moriya, N. et al. Role of the Dc domain of the bacterial hook protein FlgE in hook assembly and function. Biophysics 9, 63–72 (2013).

    CAS  Article  Google Scholar 

  19. Samatey, F. A. et al. Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism. Nature 431, 1062–1068 (2004).

    CAS  Article  Google Scholar 

  20. Matsunami, H., Barker, C. S., Yoon, Y.-H. H., Wolf, M. & Samatey, F. A. Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Nat. Commun. 7, 13425 (2016).

    CAS  Article  Google Scholar 

  21. Sakai, T., Inoue, Y., Terahara, N., Namba, K. & Minamino, T. A triangular loop of domain D1 of FlgE is essential for hook assembly but not for the mechanical function. Biochem. Biophys. Res. Commun. 495, 1789–1794 (2018).

    CAS  Article  Google Scholar 

  22. Fujii, T., Matsunami, H., Inoue, Y. & Namba, K. Evidence for the hook supercoiling mechanism of the bacterial flagellum. Biophys. Phys. 15, 28–32 (2018).

    CAS  Article  Google Scholar 

  23. Yonekura, K., Maki-Yonekura, S. & Namba, K. Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424, 643–650 (2003).

    CAS  Article  Google Scholar 

  24. Berg, H. C. Bacterial flagellar motor. Curr. Biol. 18, R689–R691 (2008).

    CAS  Article  Google Scholar 

  25. Calladine, C. R. New twists for bacterial flagella. Nat. Struct. Mol. Biol. 17, 395–396 (2010).

    CAS  Article  Google Scholar 

  26. Fujii, T., Kato, T. & Namba, K. Specific arrangement of α-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function. Structure 17, 1485–1493 (2009).

    CAS  Article  Google Scholar 

  27. Koshland, D. E., Némethy, G. & Filmer, D. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5, 365–385 (1966).

    CAS  Article  Google Scholar 

  28. Schenk, M. & Guest, S. D. On zero stiffness. Proc. Institution Mechanical Engineers C: J. Mechanical Engineering Sci. 228, 1701–1714 (2013).

    Google Scholar 

  29. Speier, C., Vogel, R. & Stark, H. Modeling the bacterial flagellum by an elastic network of rigid bodies. Phys. Biol. 8, 046009 (2011).

    CAS  Article  Google Scholar 

  30. Aizawa, S., Kato, S., Asakura, S., Kagawa, H. & Yamaguchi, S. In vitro polymerization of polyhook protein from Salmonella SJW880. Biochim. Biophys. Acta Protein Struct. 625, 291–303 (1980).

    CAS  Article  Google Scholar 

  31. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    CAS  Article  Google Scholar 

  32. Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. Elife 7, e35383 (2018).

    Article  Google Scholar 

  33. van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17–24 (1996).

    Article  Google Scholar 

  34. Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).

    CAS  Article  Google Scholar 

  35. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011).

    CAS  Article  Google Scholar 

  36. Wriggers, W. Conventions and workflows for using Situs. Acta Crystallogr. D 68, 344–351 (2012).

    CAS  Article  Google Scholar 

  37. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of COOT. Acta Crystallogr. D 66, 486–501 (2010).

    CAS  Article  Google Scholar 

  38. Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531–544 (2018).

    CAS  Article  Google Scholar 

  39. Webb, B. & Sali, A. in Protein Structure Modeling with MODELLER 39–54 (Humana Press, 2017);

  40. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

    CAS  Article  Google Scholar 

  41. Barad, B. A. et al. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015).

    CAS  Article  Google Scholar 

  42. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS  Article  Google Scholar 

  43. Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).

    CAS  Article  Google Scholar 

Download references


We thank M. Bandi for helpful discussions about the mechanical function of the hook and S.D. Aird for technical editing of the manuscript. This work was supported by the Platform Project for Supporting Drug Discovery and Life Science Research (BINDS) from AMED, under grant nos. 19am0101076 and 19am0101116 (to M.W.), by JSPS KAKENHI grants 17K17085 and 19K10083 (to S.S.) and by a JSPS KAKENHI grant 17K07318 (to H.M.). M.W. was supported by direct funding from the Okinawa Institute of Science and Technology Graduate University.

Author information

Authors and Affiliations



S.S., H.M., S.-I.A. and M.W. designed the experiments. S.S. and S.-I.A. purified the polyhooks. S.S. prepared cryo-EM specimens. S.S. and M.W. collected cryo-EM data and performed image processing. H.M. built and refined the atomic models. S.S. and H.M analyzed the structure and created figures. M.W. supervised the project. S.-I.A. and M.W. wrote the initial manuscript. All authors discussed the results and contributed to writing the paper.

Corresponding authors

Correspondence to Shin-Ichi Aizawa or Matthias Wolf.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Ines Chen was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Integrated supplementary information

Supplementary Figure 1 Polyhooks in negative stain.

Electron micrograph of negatively stained (uranyl acetate) sonicated polyhooks on carbon support film. The protein can form flat ring-like structures under these conditions. Scale bar, 100 nm.

Supplementary Figure 2 Resolution estimation.

The reconstructed electron potential map clearly resolves side chain rotamers. The map was visualized with an iso-electron potential surface contoured at 2.6σ above average. a, N-terminal α-helix. The N terminus is at the bottom. b, C-terminal α-helix. The C terminus is at the bottom. Scale bar, 10 Å. c, A Fourier shell correlation calculated with the program cisTEM between independently refined maps, each containing half of the particle images, indicates a spatial resolution of 2.9 Å (at FSC = 0.143).

Supplementary Figure 3 Polyhook model and definitions of OML and IML.

a, Space-filling atomic models of a 66-subunit assembly based on our cryo-EM map. Two protofilaments in the 11-start direction are highlighted. Subunits on the outermost line (OML) are colored cyan and those on the innermost line (IML) are pink. The top figure shows a cross-sectional view from the tip of the hook. The bottom row shows three rotated side views with the base of the hook facing down. Scale bar, 50 Å. b, Polyhook model expanded by repeating 22-subunit segments (a subset from our 66-subunit model) and fitting them end-to-end 32 times. Both colored lines are 11-start helices on the supercoiled structure. The superhelical pitch P is 996 Å, the inner radius Ri of the superhelix is 45 Å and the outer radius Ro is 252 Å. The model dimensions agree well with our experimental data (Fig. 1a,b, pitch 1,001 Å). In its natural state, the hook contains ~130 subunits (Jones, C. J. et al. J. Mol. Biol. 212, 377–387, 1990), corresponding to a ~55 nm length (Aizawa, S.-I. The Flagellar World, Academic Press, 2014). Scale bar, 20 nm.

Supplementary Figure 4 Multiple sequence alignment of hinge regions.

The amino acid sequences of FlgE proteins from 20 bacterial species reveal shared hinge motifs. They are grouped by their flagellar position: peritrichous, polar and periplasmic (PP). Seventeen are Gram-negative and three are Gram-positive (Bacillus, Clostridium and Actinoplanes).

Supplementary Figure 5 D1–loop–D2 interface. Single protofilaments are shown at OML (left, cyan) and IML (right, pink).

Subunits on the same protofilament have the same conformation. The D1 loop is colored tan, and close-up views are shown in the insets. Although it appears that the D1 loop is close to the D2 domain from the next subunit (bottom right corners of insets), only a single polar interaction was identified. All other inter-atomic distances between these two domains are more than 3.6 Å apart.

Supplementary information

Supplementary Information

Supplementary Figs. 1–5 and Supplementary Table 1.

Reporting Summary

Supplementary Video 1

Domain motions of the 11 protomers from one helical turn when aligned on D0. The animated figure was created with Pymol (Schrödinger).

Supplementary Video 2

Animation of the rotating hook, created by cyclically replacing the positions of the 11 protofilaments and morphing between their states. The movie was created with UCSF Chimera (Pettersen, E. F. et al. J. Comput. Chem. 25, 2004). First half: animation of full hook assembly. One protofilament is highlighted in orange. Second half: animation of a single protofilament.

Supplementary Video 3

Animated GIF of three classes from final 3D refinement. The superhelical structures from the three classes in the final multi-class 3D refinement iteration differed only slightly. Top row: Central slices through the 3D volume in orthogonal directions. Bottom row: Maximum intensity projections in the same directions. The spatial resolutions of these reconstructions were 3.3 Å, 3.3 Å and 3.0 Å. The subset of particle images from the reconstruction with the highest resolution was selected and refined further individually to obtain the final result at 2.9 Å resolution (Fig. 1). The images were created with cisTEM (Grant, T. et al. Elife 7, 2018).

Source data

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shibata, S., Matsunami, H., Aizawa, SI. et al. Torque transmission mechanism of the curved bacterial flagellar hook revealed by cryo-EM. Nat Struct Mol Biol 26, 941–945 (2019).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing