9LJK | pdb_00009ljk

Structure of the periplasmic domain of MotS from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.217 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9LJK

This is version 1.1 of the entry. See complete history

Literature

Sodium-Dependent Conformational Change in Flagellar Stator Protein MotS from Bacillus subtilis.

Takekawa, N.Yamaguchi, A.Nishiuchi, K.Uehori, M.Kinoshita, M.Minamino, T.Imada, K.

(2025) Biomolecules 15

  • DOI: https://doi.org/10.3390/biom15020302
  • Primary Citation Related Structures: 
    9LJK, 9LJL, 9LJM

  • PubMed Abstract: 

    The bacterial flagellar motor consists of a rotor and stator units and is driven by ion flow through the stator. The activation of the ion flow is coupled with the anchoring of the stator units to the peptidoglycan layer by the stator B-subunit around the rotor. Gram-negative bacteria, such as Salmonella and Vibrio , change the conformation of the N-terminal helix of the periplasmic domain of the B-subunit to anchor the stator units. However, a recent high-speed atomic force microscopic study has suggested that the periplasmic domain of MotS, the stator B-subunit of the sodium (Na + )-driven stator of Bacillus subtilis , a gram-positive bacterium, unfolds at low external Na + concentrations and folds at high Na + concentrations to anchor the stator units. Here, we report the crystal structures of MotS 68-242 , a periplasmic fragment of MotS, from B. subtilis at high and low Na + concentrations. We also performed far-UV CD spectroscopic analysis of the wild-type MotS 68-242 and MotS 78-242 proteins and mutant variants of MotS 68-242 under high and low Na + concentrations and found that the N-terminal disordered region of MotS 68-242 shows a Na + -dependent coil-helix transition. We propose a mechanism of the Na + -dependent structural transition of Bs-MotS to anchor the stator units.


  • Organizational Affiliation
    • Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan.

Macromolecule Content 

  • Total Structure Weight: 41.9 kDa 
  • Atom Count: 2,734 
  • Modeled Residue Count: 309 
  • Deposited Residue Count: 364 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Flagellar motor protein MotS
A, B
182Bacillus subtilisMutation(s): 0 
Gene Names: motSP5633_09250
UniProt
Find proteins for P39064 (Bacillus subtilis (strain 168))
Explore P39064 
Go to UniProtKB:  P39064
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39064
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.217 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.99α = 90
b = 80.73β = 100.44
c = 55.24γ = 90
Software Package:
Software NamePurpose
BSSdata collection
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23K18114
Japan Society for the Promotion of Science (JSPS)Japan21H02443
Japan Society for the Promotion of Science (JSPS)Japan17KT0026
Japan Society for the Promotion of Science (JSPS)Japan23K14158

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references