5H5V

Crystal structure of the flagellar cap protein FliD D1-D2-D3 domains from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Self-Oligomerizing Structure of the Flagellar Cap Protein FliD and Its Implication in Filament Assembly.

Song, W.S.Cho, S.Y.Hong, H.J.Park, S.C.Yoon, S.I.

(2017) J. Mol. Biol. 429: 847-857

  • DOI: 10.1016/j.jmb.2017.02.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • FliD is a self-oligomerizing structural protein that caps the growing end of the bacterial flagellar filament. FliD also plays a key role in the flagellar system by continuously adding a new flagellin protein to the tip of the filament. To structural ...

    FliD is a self-oligomerizing structural protein that caps the growing end of the bacterial flagellar filament. FliD also plays a key role in the flagellar system by continuously adding a new flagellin protein to the tip of the filament. To structurally characterize FliD oligomerization and to provide a FliD-mediated flagellin polymerization mechanism, we have determined the crystal structures of FliD proteins from Escherichia coli and Salmonella enterica serovar Typhimurium (ecFliD and stFliD, respectively). ecFliD consists of three domains (D1, D2, and D3) and forms a hexamer plate of the D2 and D3 domains that resembles a six-pointed star with legs consisting of the D1 domain. In contrast, the D2 and D3 domains of stFliD assemble into a pentamer as a five-pointed star plate. Despite their distinct oligomeric states, ecFliD and stFliD engage a common molecular surface for oligomerization. FliD also features interdomain and intersubunit flexibility, suggesting that FliD reorganizes its domains and adjacent subunits depending on the FliD binding partner. The similarity of the FliD shape to flagellin and the structural dynamics of FliD led us to propose a FliD-catalyzed filament elongation mechanism. In this model, FliD occupies a position in place of a nascent flagellin until the flagellin reaches the growing end of the filament, and then, FliD moves aside to repeat the positional replacement.


    Organizational Affiliation

    Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea. Electronic address: sungil@kangwon.ac.kr.,Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flagellar hook-associated protein 2
A, B, C, D, E, F
380Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fliD (flaV, flbC)
Find proteins for P24216 (Escherichia coli (strain K12))
Go to UniProtKB:  P24216
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.062α = 90.00
b = 181.582β = 105.23
c = 110.456γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references