Molecular structure of the intact bacterial flagellar basal body

Steven Johnson, Emily J. Furlong, Justin C. Deme, Ashley L. Nord, Joseph Caesar, Fabienne F.V. Chevance, Richard M. Berry, Kelly T. Hughes, Susan M. Lea

Preprint posted on 6 December 2020

Article now published in Nature Microbiology at

Johnson et al. resolve the high-resolution cryo-EM structure of the intact flagellar basal body from Salmonella

Selected by NYUPeerReview

Categories: biophysics, microbiology


Bacterial and prokaryotic motility often depend on physical appendages called flagella, which protrude from the organism’s membrane and initiate motion through rotational movement, propelling the organism in a directional manner. This movement is important for the organism’s survival and fitness. The flagellar basal body is located at the base of the flagellum, and is important for assembling the flagellum as well as facilitating rotational movement. The basal body is composed of a complex network of transmembrane proteins that form rings and anchor flagellar components to the bacterial inner and outer membranes and the intervening cell wall in Gram-negative bacteria (Figure 1). Flagellar rotation is generated by proton flow from the periplasm through the stator, which rotates the C-ring. Rotation of the C-ring, which is coupled to the axial rod (the portion of the flagellum that transverses the inner and outer membranes and cell wall), drives flagellar motion. Previous genetic and biophysical studies have partially characterized the role of many constituent flagellar components, including rotational dynamics and structural arrangement in the bacterial membrane. Low resolution structures obtained from cryo-electron tomography have identified key complexes that form the basal body, outlining the rough positioning of its components, and high-resolution insights of some basal body subcomplexes such as portions of the axial rod and cap protein are also available. However, a high resolution structure of the entire basal body is not available, and represents a gap in our knowledge of how this large and complex protein machine may function. In this preprint, Johnson et al. resolve the cryo-EM structure of the intact Salmonella flagellar basal body at high resolution (Figure 2). This is a stunning structure of an immensely large multi-protein complex, providing exciting new insights into the structure of the axial rod and the outer membrane “bushing” complex, and how the 173 protein components of the basal body assemble to enable flagellar rotation.

Image credit: Mariana Ruiz Villarreal via Wikipedia (left diagram) and Figures 1, 2, and 3 from Johnson et al.


Key Findings

●  Cryo EM structure of the fully assembled flagellar basal body, including the LP-ring, the MS-ring, and the rod proteins at a 2.2-3.7 Å resolution. This includes a ~2.2 Å resolution reconstruction of the OM “bushing” complex, consisting of 26 copies each of FlgH, FlgI, and YecR.

●  Identification of a lipoprotein protein YecR, bound to the outer surfaces of the LP-ring, proposed to play a role in the assembly of the LP-ring by modulating interactions with lipids in the surrounding membrane.

●  Components of the axial rod and their respective symmetries are resolved. Comparison of this structure of the export gate and associated axial rod with a previously determined cryo-EM structure of an isolated axial rod export gate in the closed state, revealed a possible mechanism by which the gate may open to allow flagellar components to be secreted through the periplasm and outer membrane.

●  The intact hook cap complex, which is responsible for organizing the secretion and assembly of hook proteins was resolved. In comparison to previous models suggesting that the cap protein would rotate as new proteins were added to the growing filament, this work suggests that the cap protein is not rotating but rather undergoing a stepping motion tracking the growing tip. The hook cap complex forms a loosely associated pentameric structure that allows for the addition of hook cap proteins to the nascent hook in a “stepped revolution” fashion.

●  The detail of this structure improves our understanding of the interactions between the axial rod and ring component interfaces in the basal body. Analysis of these interactions at the molecular level provides an explanation for the discontinuous rotation of the flagellum in 26 discrete steps based upon the 26-fold symmetry of the LP-ring complex.

Why we chose this preprint

While previous studies have characterized individual components of flagellar assembly or have reconstructed large complexes at modest resolution, this structural analysis provides a high resolution map of intact flagellar basal bodies with sufficient detail to hypothesize the mechanism of flagellar assembly and secretion of flagellar components. Understanding modes of secretion and assembly of the flagellum better our understanding of bacterial motility and even pathogenesis. Additionally, achieving such high resolution structures complex molecular machine is impressive and will be of broad interest to the microbiology field.

Questions for the authors

●  How does the Salmonella basal body compare to flagella from other bacterial species? Are the core components of this structure broadly conserved?

●  Could this work be used for the future development of molecules that target the flagellar basal body assembly and potentially drug development?

●  At what point in basal flagellar assembly does a proton gradient drive rotation? At what point are these components sufficiently assembled to enable rotation? For example, can hook and flagellin assembly occur while the system is rotating?

●  What was the most challenging aspect of this study?



  1. Andreas Diepold and Judith P. Armitage. Type III secretion systems: the bacterial flagellum and the injectisome. Philos Trans R Soc Lond B Biol Sci. 370:20150020 (2015)
  2. Takashi Fujii, Takayuki Kato, Koichi D. Hiraoka, Tomoko Miyata, Tohru Minamino, Fabienne F. V. Chevance, Kelly T. Hughes & Keiichi Namba. Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook. Nat Comm 8:14276 (2017)
  3. Yumiko Saijo-Hamano, Hideyuki Matsunami, Keiichi Namba, Katsumi Imada. Architecture of the Bacterial Flagellar Distal Rod and Hook of Salmonella. Biomolecules. 9:260. (2019)
  4. Mariana Ruiz Villarreal, Flagellum diagram,
  5. Steven Johnson, Emily J. Furlong, Justin C. Deme, Ashley L. Nord, Joseph Caesar, Fabienne F.V. Chevance, Richard M. Berry, Kelly T. Hughes, Susan M. Lea. Molecular structure of the intact bacterial flagellar basal body.bioRxiv 2020.12.05.413195; doi:


Posted on: 6 April 2021 , updated on: 21 April 2021

doi: Pending

Read preprint (No Ratings Yet)

Have your say

Your email address will not be published.

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here