4I1K

Crystal Structure of VRN1 (Residues 208-341)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Arabidopsis B3 Domain Protein VERNALIZATION1 (VRN1) Is Involved in Processes Essential for Development, with Structural and Mutational Studies Revealing Its DNA-binding Surface.

King, G.J.Chanson, A.H.McCallum, E.J.Ohme-Takagi, M.Byriel, K.Hill, J.M.Martin, J.L.Mylne, J.S.

(2013) J.Biol.Chem. 288: 3198-3207

  • DOI: 10.1074/jbc.M112.438572

  • PubMed Abstract: 
  • The B3 DNA-binding domain is a plant-specific domain found throughout the plant kingdom from the alga Chlamydomonas to grasses and flowering plants. Over 100 B3 domain-containing proteins are found in the model plant Arabidopsis thaliana, and one of ...

    The B3 DNA-binding domain is a plant-specific domain found throughout the plant kingdom from the alga Chlamydomonas to grasses and flowering plants. Over 100 B3 domain-containing proteins are found in the model plant Arabidopsis thaliana, and one of these is critical for accelerating flowering in response to prolonged cold treatment, an epigenetic process called vernalization. Despite the specific phenotype of genetic vrn1 mutants, the VERNALIZATION1 (VRN1) protein localizes throughout the nucleus and shows sequence-nonspecific binding in vitro. In this work, we used a dominant repressor tag that overcomes genetic redundancy to show that VRN1 is involved in processes beyond vernalization that are essential for Arabidopsis development. To understand its sequence-nonspecific binding, we crystallized VRN1(208-341) and solved its crystal structure to 1.6 Å resolution using selenium/single-wavelength anomalous diffraction methods. The crystallized construct comprises the second VRN1 B3 domain and a preceding region conserved among VRN1 orthologs but absent in other B3 domains. We established the DNA-binding face using NMR and then mutated positively charged residues on this surface with a series of 16 Ala and Glu substitutions, ensuring that the protein fold was not disturbed using heteronuclear single quantum correlation NMR spectra. The triple mutant R249E/R289E/R296E was almost completely incapable of DNA binding in vitro. Thus, we have revealed that although VRN1 is sequence-nonspecific in DNA binding, it has a defined DNA-binding surface.


    Organizational Affiliation

    Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B3 domain-containing transcription factor VRN1
A, B
146Arabidopsis thalianaMutation(s): 0 
Gene Names: VRN1
Find proteins for Q8L3W1 (Arabidopsis thaliana)
Go to UniProtKB:  Q8L3W1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.120 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.152α = 90.00
b = 47.310β = 114.97
c = 61.413γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
AutoSolphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2013-02-20
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Advisory, Refinement description