6AI2 | pdb_00006ai2

Structure of the 328-692 fragment of FlhA (F459A)

• PDB DOI: https://doi.org/10.2210/pdb6AI2/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Salmonella enterica subsp. enterica serovar Typhimurium
• Mutation(s): Yes 


• Deposited: 2018-08-21 Released: 2019-03-20 
• Deposition Author(s): Ogawa, Y., Kinoshita, M., Minamino, T., Imada, K.
• Funding Organization(s): Japan Society for the Promotion of Science, Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus.

Inoue, Y., Ogawa, Y., Kinoshita, M., Terahara, N., Shimada, M., Kodera, N., Ando, T., Namba, K., Kitao, A., Imada, K., Minamino, T.

(2019) Structure 27: 965

• PubMed: 31031200 
• DOI: https://doi.org/10.1016/j.str.2019.03.017
• Primary Citation Related Structures: 
  6AI0, 6AI1, 6AI2, 6AI3


• PubMed Abstract: 
  

  Bacteria use a type III protein export apparatus for construction of the flagellum, which consists of the basal body, the hook, and the filament. FlhA forms a homo-nonamer through its C-terminal cytoplasmic domains (FlhA _C ) and ensures the strict order of flagellar assembly. FlhA _C goes through dynamic domain motions during protein export, but it remains unknown how it occurs. Here, we report that the FlhA(G368C) mutation biases FlhA _C toward a closed form, thereby reducing the binding affinity of FlhA _C for flagellar export chaperones in complex with their cognate filament-type substrates. The G368C mutations also restrict the conformational flexibility of a linker region of FlhA (FlhA _L ), suppressing FlhA _C ring formation. We propose that interactions of FlhA _L with its neighboring subunit converts FlhA _C in the ring from a closed conformation to an open one, allowing the chaperon/substrate complexes to bind to the FlhA _C ring to form the filament at the hook tip.

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Organizational Affiliation: 
• Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; RIKEN Center for Biosystems Dynamics Research & SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan. Electronic address: [e-mail].
Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan. Electronic address: [e-mail].
Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.19 kDa 
• Atom Count: 5,334 
• Modeled Residue Count: 690 
• Deposited Residue Count: 738 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar biosynthesis protein FlhA	A, B	369	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	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: 3.30 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 216.39	α = 90
b = 216.39	β = 90
c = 65.33	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Ogawa, Y., Kinoshita, M., Minamino, T., Imada, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP15H02386
Japan Society for the Promotion of Science	Japan	JP26293097
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP23115008
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP24117004
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP25121718
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP15H01640

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Database references
• Version 1.2: 2019-06-19
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description