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 1.1 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: https://doi.org/10.1074/jbc.M111.279844
  • Primary Citation of Related Structures:  
    2LEX

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable WRKY transcription factor 478Arabidopsis thalianaMutation(s): 0 
Gene Names: WRKY4
UniProt
Find proteins for Q9XI90 (Arabidopsis thaliana)
Explore Q9XI90 
Go to UniProtKB:  Q9XI90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XI90
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*G*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')16N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*GP*C*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*CP*G)-3')16N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations