9JQO | pdb_00009jqo

Polyrod formed by FlgG (G65V) from the Salmonella TH26292 strain

• PDB DOI: https://doi.org/10.2210/pdb9JQO/pdb
• EM Map EMD-61731: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Salmonella enterica subsp. enterica serovar Typhimurium
• Mutation(s): Yes 


• Deposited: 2024-09-27 Released: 2026-02-04 
• Deposition Author(s): Yamaguchi, T., Kato, T., Minamino, T., Namba, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

Structural insights into the assembly mechanism of the molecular bushing in the bacterial flagellar motor.

Yamaguchi, T., Minamino, T., Kato, T., Chevance, F.F.V., Hughes, K.T., Namba, K.

(2026) Commun Biol 

• PubMed: 42443432 
• DOI: https://doi.org/10.1038/s42003-026-10640-y
• Primary Citation Related Structures: 
  9IYC, 9JQO


• PubMed Abstract: 
  

  The LP-ring complex of the Salmonella flagellar motor acts as a bushing that supports high-speed rotation of the rod, which serves as a drive shaft. The L-ring, P-ring, and distal rod consist of FlgH, FlgI, and FlgG, respectively. LP-ring formation begins with P-ring assembly around the distal rod, where it remains firmly attached until the L-ring assembles above it. L-ring formation induces P-ring detachment, allowing the rod to freely rotate within the LP-ring, but this mechanism remains unclear. Here, we report the cryoEM structure of the P-ring assembled on a polyrod, an unusually elongated rod structure. The P-ring exhibits a slightly elliptical shape with a 2.7° tilt relative to the rod axis for its stable attachment. However, L-ring assembly on the P-ring causes steric clashes with the rod to induce P-ring detachment, allowing it to adopt a circular shape and complete the LP-ring as a functional bushing.

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Organizational Affiliation: 
• Graduate School of Frontier Biosciences, The University of Osaka, Suita, Osaka, Japan.
Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
Institute for Protein Research, The University of Osaka, Suita, Osaka, Japan.
The School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.
Graduate School of Frontier Biosciences, The University of Osaka, Suita, Osaka, Japan. [e-mail].
JEOL YOKOGUSHI Research Alliance Laboratories, The University of Osaka, Suita, Osaka, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 48-mer - A48 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,335.69 kDa 
• Atom Count: 89,976 
• Modeled Residue Count: 11,948 
• Deposited Residue Count: 12,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar basal-body rod protein FlgG	A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, X, Y, Z	260	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 1  Gene Names: flgG, fla FVII, flaL, STY1218, t1741
UniProt
Find proteins for P0A1J4 (Salmonella typhi) Explore P0A1J4  Go to UniProtKB:  P0A1J4

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21rc1_5127
RECONSTRUCTION	cryoSPARC	3.2.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Yamaguchi, T., Kato, T., Minamino, T., Namba, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP25000013MEXT KAKENHI Grant Number JP15H01640,JP20H05532
Japan Society for the Promotion of Science (JSPS)	Japan	JP18K06155
Japan Society for the Promotion of Science (JSPS)	Japan	JP26293097
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H03182
Japan Society for the Promotion of Science (JSPS)	Japan	JP15H01640
Japan Society for the Promotion of Science (JSPS)	Japan	Japan Society for the Promotion of Science (JSPS)
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am0101117
Japan Agency for Medical Research and Development (AMED)	Japan	JP17pc0101020
Japan Society for the Promotion of Science (JSPS)	Japan	JP21J12128

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release
  
• Version 2.0: 2026-03-04
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2026-04-29
  Changes: Data collection, Database references, Experimental preparation
• Version 2.2: 2026-06-24
  Changes: Data collection, Experimental preparation
• Version 2.3: 2026-07-29
  Changes: Data collection, Database references