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 5XRW | pdb_00005xrw

Crystal structure of flagellar motor switch complex from H. pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5XRW

This is version 1.3 of the entry. See complete history. 

Literature

Three SpoA-domain proteins interact in the creation of the flagellar type III secretion system inHelicobacter pylori.

Lam, K.H., Xue, C., Sun, K., Zhang, H., Lam, W.W.L., Zhu, Z., Ng, J.T.Y., Sause, W.E., Lertsethtakarn, P., Lau, K.F., Ottemann, K.M., Au, S.W.N.

(2018) J Biol Chem 293: 13961-13973

  • DOI: https://doi.org/10.1074/jbc.RA118.002263
  • Primary Citation Related Structures: 
    5XRW

  • PubMed Abstract: 

    Bacterial flagella are rotary nanomachines that contribute to bacterial fitness in many settings, including host colonization. The flagellar motor relies on the multiprotein flagellar motor-switch complex to govern flagellum formation and rotational direction. Different bacteria exhibit great diversity in their flagellar motors. One such variation is exemplified by the motor-switch apparatus of the gastric pathogen Helicobacter pylori , which carries an extra switch protein, FliY, along with the more typical FliG, FliM, and FliN proteins. All switch proteins are needed for normal flagellation and motility in H. pylori , but the molecular mechanism of their assembly is unknown. To fill this gap, we examined the interactions among these proteins. We found that the C-terminal SpoA domain of FliY (FliY C ) is critical to flagellation and forms heterodimeric complexes with the FliN and FliM SpoA domains, which are β-sheet domains of type III secretion system proteins. Surprisingly, unlike in other flagellar switch systems, neither FliY nor FliN self-associated. The crystal structure of the FliY C -FliN C complex revealed a saddle-shaped structure homologous to the FliN-FliN dimer of Thermotoga maritima , consistent with a FliY-FliN heterodimer forming the functional unit. Analysis of the FliY C -FliN C interface indicated that oppositely charged residues specific to each protein drive heterodimer formation. Moreover, both FliY C -FliM C and FliY C -FliN C associated with the flagellar regulatory protein FliH, explaining their important roles in flagellation. We conclude that H. pylori uses a FliY-FliN heterodimer instead of a homodimer and creates a switch complex with SpoA domains derived from three distinct proteins.


  • Organizational Affiliation: 
    • From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong.

Macromolecule Content 

  • Total Structure Weight: 34.85 kDa 
  • Atom Count: 2,486 
  • Modeled Residue Count: 315 
  • Deposited Residue Count: 316 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FliN
A, B
79Helicobacter pylori 26695Mutation(s): 0 
UniProt
Find proteins for O25306 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25306 
Go to UniProtKB:  O25306
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25306
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FliY
C, D
79Helicobacter pylori 26695Mutation(s): 0 
UniProt
Find proteins for O25674 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25674 
Go to UniProtKB:  O25674
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25674
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.21α = 69.34
b = 49.21β = 82.98
c = 52.37γ = 76.01
Software Package:
Software NamePurpose
MOSFLMdata collection
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Grants CouncilHong KongN_CUHK454/13
NSFCChina31370713

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Refinement description