2LEX

Complex of the C-terminal WRKY domain of AtWRKY4 and a W-box DNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for sequence-spscific DNA recognition by an Arabidopsis WRKY transcription factor

Yamasaki, K.Kigawa, T.Watanabe, S.Inoue, M.Yamasaki, T.Seki, M.Shinozaki, K.Yokoyama, S.

(2012) J.Biol.Chem. --: --

  • DOI: 10.1074/jbc.M111.279844

  • PubMed Abstract: 
  • The WRKY family transcription factors regulate plant-specific reactions that are mostly related to biotic and abiotic stresses. They share the WRKY domain, which recognizes a DNA element (TTGAC(C/T)) termed the W-box, in target genes. Here, we determ ...

    The WRKY family transcription factors regulate plant-specific reactions that are mostly related to biotic and abiotic stresses. They share the WRKY domain, which recognizes a DNA element (TTGAC(C/T)) termed the W-box, in target genes. Here, we determined the solution structure of the C-terminal WRKY domain of Arabidopsis WRKY4 in complex with the W-box DNA by NMR. A four-stranded β-sheet enters the major groove of DNA in an atypical mode termed the β-wedge, where the sheet is nearly perpendicular to the DNA helical axis. Residues in the conserved WRKYGQK motif contact DNA bases mainly through extensive apolar contacts with thymine methyl groups. The importance of these contacts was verified by substituting the relevant T bases with U and by surface plasmon resonance analyses of DNA binding.


    Organizational Affiliation

    National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan. k-yamasaki@aist.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable WRKY transcription factor 4
A
78Arabidopsis thalianaGene Names: WRKY4
Find proteins for Q9XI90 (Arabidopsis thaliana)
Go to UniProtKB:  Q9XI90
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*G*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')B16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*C*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*CP*G)-3')C16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 
  • Olderado: 2LEX Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release