3TND

Crystal structure of Shigella flexneri VapBC toxin-antitoxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the VapBC Toxin-Antitoxin Complex from Shigella flexneri Reveals a Hetero-Octameric DNA-Binding Assembly.

Dienemann, C.Boggild, A.Winther, K.S.Gerdes, K.Brodersen, D.E.

(2011) J.Mol.Biol. 414: 713-722

  • DOI: 10.1016/j.jmb.2011.10.024

  • PubMed Abstract: 
  • Toxin-antitoxin (TA) loci are common in archaea and prokaryotes and allow cells to rapidly adapt to changing environmental conditions through release of active regulators of metabolism. Many toxins are endonucleases that target cellular mRNA and tRNA ...

    Toxin-antitoxin (TA) loci are common in archaea and prokaryotes and allow cells to rapidly adapt to changing environmental conditions through release of active regulators of metabolism. Many toxins are endonucleases that target cellular mRNA and tRNAs, while the antitoxins tightly wrap around the toxins to inhibit them under normal circumstances. The antitoxins also bind to operators in the promoter regions of the cognate TA operon and thereby regulate transcription. For enteric vapBC TA loci, the VapC toxins specifically cleave tRNA(fMet) and thus down-regulate protein synthesis. Here, we describe the crystal structure of the intact Shigella flexneri VapBC TA complex, determined to 2.7 Å resolution. Both in solution and in the crystal structure, four molecules of each protein combine to form a large and globular hetero-octameric assembly with SpoVT/AbrB-type DNA-binding domains at each end and a total molecular mass of about 100 kDa. The structure gives new insights into the inhibition of VapC toxins by VapB and provides the molecular basis for understanding transcriptional regulation through VapB dimerization.


    Organizational Affiliation

    Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA(fMet)-specific endonuclease VapC
A, C, E, G
132Shigella flexneriMutation(s): 0 
Gene Names: vapC (mvpA, stborf2)
EC: 3.1.-.-
Find proteins for O06662 (Shigella flexneri)
Go to UniProtKB:  O06662
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antitoxin VapB
B, D, F, H
81Shigella flexneriMutation(s): 0 
Gene Names: vapB
Find proteins for O06663 (Shigella flexneri)
Go to UniProtKB:  O06663
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D, E, F, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.403α = 90.00
b = 91.403β = 90.00
c = 549.090γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
DNAdata collection
PHENIXrefinement
SOLVEphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Database references
  • Version 1.2: 2011-12-21
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Data collection