2LEX | pdb_00002lex

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

• PDB DOI: https://doi.org/10.2210/pdb2LEX/pdb
• NAKB: 2LEX
• BMRB: 17732

• Classification: TRANSCRIPTION/DNA
• Organism(s): Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 2011-06-24 Released: 2012-01-18 
• Deposition Author(s): Yamasaki, K., Kigawa, T., Watanabe, S., Inoue, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

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

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 Biological Chem 

• PubMed: 22219184 
• DOI: https://doi.org/10.1074/jbc.M111.279844
• Primary Citation 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.

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Organizational Affiliation: 
• National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.45 kDa 
• Atom Count: 913 
• Modeled Residue Count: 83 
• Deposited Residue Count: 110 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

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
UniProt
Find proteins for Q9XI90 (Arabidopsis thaliana) Explore Q9XI90  Go to UniProtKB:  Q9XI90

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*G*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)-3')	B	16	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*C*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*CP*G)-3')	C	16	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Yamasaki, K., Kigawa, T., Watanabe, S., Inoue, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

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