9LRZ | pdb_00009lrz

Core filament of the spirochete periplasmic flagella of Leptospira biflexa

• PDB DOI: https://doi.org/10.2210/pdb9LRZ/pdb
• EM Map EMD-63348: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Leptospira biflexa
• Mutation(s): No 


• Deposited: 2025-02-02 Released: 2025-12-24 
• Deposition Author(s): Kawamoto, A., Nakamura, S., Koizumi, N.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Asymmetric sheath coordination controls flagellar architecture and function in Leptospira spirochete.

Kawamoto, A., Kuribayashi, T., Morita, M., Nakamura, S., Koizumi, N.

(2026) EMBO J 45: 2882-2904

• PubMed: 41844841 
• DOI: https://doi.org/10.1038/s44318-026-00731-1
• Primary Citation Related Structures: 
  9LRY, 9LRZ, 9LS0, 9LS1, 9X7K, 9X7L, 9X7M, 9X7S, 9X7V, 9X80


• PubMed Abstract: 
  

  Bacterial flagella are essential for motility, but their structure and how they generate movement vary greatly. Most motile bacteria use external helical flagella, whereas spirochetes have periplasmic flagella (PFs) that distort the cell body to drive forward movement. Here, we generated sheath protein knockout mutants and used high-resolution cryo-electron microscopy to elucidate the mechanisms underlying PF assembly, curvature, and rigidity in Leptospira biflexa. The PF consists of a FlaB1-based core filament surrounded asymmetrically by sheath proteins. Weak but essential binding of FlaA2 to the core enables asymmetric localization of the coiling protein FcpA. FcpA alone can induce curvature, whereas FcpB acts as a structural wedge that reinforces PF rigidity and enables efficient swimming in liquid. Specific glycosylation of FlaB1 mediates sheath-core interactions and may guide the assembly of sheath components. We propose that sheath proteins interact transiently with the core and may be anchored to the outer membrane, allowing core rotation beneath a static sheath. These findings reveal how cooperative interactions among sheath components confer structural and mechanical specialization to spirochete flagella.

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Organizational Affiliation: 
• Institute for Protein Research, The University of Osaka, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. [e-mail].
Department of Applied Physics, Graduate School of Engineering, Tohoku University, 6-6-05 Aoba, Aoba, Sendai, Miyagi, 980-8579, Japan.
Department of Bacteriology I, National Institute of Infectious Diseases, Japan Institute for Health Security, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan.
Department of Applied Physics, Graduate School of Engineering, Tohoku University, 6-6-05 Aoba, Aoba, Sendai, Miyagi, 980-8579, Japan. [e-mail].
Department of Bacteriology I, National Institute of Infectious Diseases, Japan Institute for Health Security, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 31.27 kDa 
• Atom Count: 2,172 
• Modeled Residue Count: 280 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellin	A	281	Leptospira biflexa	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.3
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Kawamoto, A., Nakamura, S., Koizumi, N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24K02274
Japan Science and Technology	Japan	JPMJPR21E5

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release
  
• Version 1.1: 2026-07-08
  Changes: Data collection, Database references