9LUB | pdb_00009lub

The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 2

• PDB DOI: https://doi.org/10.2210/pdb9LUB/pdb
• EM Map EMD-63393: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Paenibacillus sp. TCA20, Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2025-02-08 Released: 2025-04-09 
• Deposition Author(s): Onoe, S., Nishikino, T., Kinoshita, M., Kishikawa, J., Kato, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM Structure of the Flagellar Motor Complex from Paenibacillus sp. TCA20.

Onoe, S., Nishikino, T., Kinoshita, M., Takekawa, N., Minamino, T., Imada, K., Namba, K., Kishikawa, J.I., Kato, T.

(2025) Biomolecules 15

• PubMed: 40149971 
• DOI: https://doi.org/10.3390/biom15030435
• Primary Citation Related Structures: 
  9LU9, 9LUB, 9LUC


• PubMed Abstract: 
  

  The bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. The flagellar motor is composed of a rotor and stator complexes, with each stator unit functioning as an ion channel that converts flow from outside of cell membrane into rotational motion. Paenibacillus sp. TCA20 was discovered in a hot spring, and a structural analysis was conducted on the stator complex using cryo-electron microscopy to elucidate its function. Two of the three structures (Classes 1 and 3) were found to have structural properties typical for other stator complexes. In contrast, in Class 2 structures, the pentamer ring of the A subunits forms a C-shape, with lauryl maltose neopentyl glycol (LMNG) bound to the periplasmic side of the interface between the A and B subunits. This interface is conserved in all stator complexes, suggesting that hydrophobic ligands and lipids can bind to this interface, a feature that could potentially be utilized in the development of novel antibiotics aimed at regulating cell motility and infection.

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Organizational Affiliation: 
• Institute for Protein Research, Osaka University, Suita 565-0871, Osaka, Japan.
Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Aichi, Japan.
OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya 466-8555, Aichi, Japan.
Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Osaka, Japan.
JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita 565-0871, Osaka, Japan.
Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan.
Faculty of Applied Biology, Kyoto Institute of Technology, Kyoto 606-8585, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A5B2 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 213.37 kDa 
• Atom Count: 10,113 
• Modeled Residue Count: 1,326 
• Deposited Residue Count: 1,958 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar motor protein MotA	A, B, C, D, E	264	Paenibacillus sp. TCA20	Mutation(s): 0  Gene Names: TCA2_3717 Membrane Entity: Yes
UniProt
Find proteins for A0AAX3N6G0 (Paenibacillus urinalis) Explore A0AAX3N6G0  Go to UniProtKB:  A0AAX3N6G0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric B subunit of MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E. coli,Motility protein B	F, G	319	Paenibacillus sp. TCA20, Escherichia coli This entity is chimeric	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0AF06 (Escherichia coli (strain K12)) Explore P0AF06  Go to UniProtKB:  P0AF06

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat
RECONSTRUCTION	cryoSPARC	3.8

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Onoe, S., Nishikino, T., Kinoshita, M., Kishikawa, J., Kato, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101XXX.
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K14157

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release