Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.65 kDa 
• Atom Count: 569 
• Modelled Residue Count: 71 
• Deposited Residue Count: 78 
• Unique protein chains: 1

1WJ2

Solution Structure of the C-terminal WRKY Domain of AtWRKY4

• PDB DOI: 10.2210/pdb1WJ2/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 2004-05-28 Released: 2004-11-28 
• Deposition Author(s): Yamasaki, K., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of an Arabidopsis WRKY DNA binding domain.

Yamasaki, K., Kigawa, T., Inoue, M., Tateno, M., Yamasaki, T., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Tomo, Y., Hayami, N., Terada, T., Shirouzu, M., Tanaka, A., Seki, M., Shinozaki, K., Yokoyama, S.

(2005) Plant Cell 17: 944-956

• PubMed: 15705956 
• DOI: 10.1105/tpc.104.026435
• Primary Citation of Related Structures:  
  1WJ2


• PubMed Abstract: 
  

The WRKY proteins comprise a major family of transcription factors that are essential in pathogen and salicylic acid responses of higher plants as well as a variety of plant-specific reactions. They share a DNA binding domain, designated as the WRKY domain, which contains an invariant WRKYGQK sequence and a CX4-5CX22-23HXH zinc binding motif. Herein, we report the NMR solution structure of the C-terminal WRKY domain of the Arabidopsis thaliana WRKY4 protein. The structure consists of a four-stranded beta-sheet, with a zinc binding pocket formed by the conserved Cys/His residues located at one end of the beta-sheet, revealing a novel zinc and DNA binding structure. The WRKYGQK residues correspond to the most N-terminal beta-strand, kinked in the middle of the sequence by the Gly residue, which enables extensive hydrophobic interactions involving the Trp residue and contributes to the structural stability of the beta-sheet. Based on a profile of NMR chemical shift perturbations, we propose that the same strand enters the DNA groove and forms contacts with the DNA bases.

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Organizational Affiliation: 

Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable WRKY transcription factor 4	A	78	Arabidopsis thaliana	Mutation(s): 0  Gene Names: WRKY4, At1g13960, F16A14.18, F7A19.5
UniProt
Find proteins for Q9XI90 (Arabidopsis thaliana) Explore Q9XI90  Go to UniProtKB:  Q9XI90

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1WJ2 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-28 
• Released Date: 2004-11-28 
Deposition Author(s): Yamasaki, K., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-11-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations