23TK | pdb_000023tk

Structure of the 328-692 fragment of FlhA (A489E) form 1

• PDB DOI: https://doi.org/10.2210/pdb23TK/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2026-02-16 Released: 2026-10-07 
• Deposition Author(s): Sakai, M., Kinoshita, M., Takekawa, N., Minamino, T., Imada, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.262 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

Structural basis for substrate specificity switching revealed by the FlhA(A489E) suppressor mutation.

Sakai, M., Kinoshita, M., Takekawa, N., Namba, K., Imada, K., Minamino, T.

(2026) Biophys Physicobiol 23: e230030-e230030

• PubMed: 42840504 
• DOI: https://doi.org/10.2142/biophysico.bppb-v23.0030
• Primary Citation Related Structures: 
  23TK, 23TM


• PubMed Abstract: 
  

  The flagellar type III secretion system (fT3SS) switches its substrate specificity from hook-type to filament-type upon completion of hook assembly. This process is regulated by the coordinated actions of FliK, FlhB, and FlhA, but the structural mechanism underlying substrate specificity switching remains unclear. Here, we determined the crystal structures of the C-terminal cytoplasmic domain of FlhA(FlhA _C ) carrying the A489E substitution, which partially restores motility of the cleavage-defective flhB (P270A) mutant. The structures were solved in two distinct conformational states: an open form at 3.28 Å resolution and a semi-closed form at 2.90 Å resolution. In parallel, AlphaFold3-based structural predictions suggested that the flexible C-terminal cytoplasmic tail of FlhB (FlhB _CCT ) binds to a groove formed between the α2 helix and β2 strand of FlhA _C , overlapping with the intersubunit linker-binding site within the FlhA _C ring. Structural analyses further revealed that the A489E substitution rearranges a local salt-bridge network involving Arg-386 and Glu-483, leading to subtle positional shifts of the α2 helix and remodeling of the predicted FlhB _CCT -binding surface. These structural changes may alter the predicted interaction between FlhA _C and FlhB _CCT , thereby lowering the energetic barrier associated with conformational remodeling of the FlhA _C ring during substrate specificity switching. Together, our results provide structural insight into how local electrostatic remodeling modulates conformational dynamics of FlhA _C and regulates substrate specificity switching in the fT3SS.

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Organizational Affiliation: 
• Department of Macromolecular Science, Graduate School of Science, The University of Osaka, Toyonaka, Osaka 560-0043, Japan.
Graduate School of Frontier Biosciences, The University of Osaka, Suita, Osaka 565-0871, Japan.
JEOL YOKOGUSHI Research Alliance Laboratories, The University of Osaka, Suita, Osaka 565-0871, Japan.
Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 86.63 kDa 
• Atom Count: 5,183 
• Modeled Residue Count: 669 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthesis protein FlhA	A, B	389	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 1  Gene Names: flhA, STM1913
UniProt
Find proteins for P40729 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P40729  Go to UniProtKB:  P40729

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.262 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.24	α = 90
b = 93.25	β = 90
c = 187.28	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-07 
Deposition Author(s): Sakai, M., Kinoshita, M., Takekawa, N., Minamino, T., Imada, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K15749
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K06162
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H03182
Japan Society for the Promotion of Science (JSPS)	Japan	JP22H02573
Japan Society for the Promotion of Science (JSPS)	Japan	15H02386
Japan Society for the Promotion of Science (JSPS)	Japan	21H02443

Revision History  

• Version 1.0: 2026-10-07
  Type: Initial release
  
• Version 1.1: 2026-10-21
  Changes: Database references