1WIJ | pdb_00001wij

Solution Structure of the DNA-Binding Domain of Ethylene-Insensitive3-Like3

• PDB DOI: https://doi.org/10.2210/pdb1WIJ/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 the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3.

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

(2005) J Mol Biology 348: 253-264

• PubMed: 15811366 
• DOI: https://doi.org/10.1016/j.jmb.2005.02.065
• Primary Citation Related Structures: 
  1WIJ


• PubMed Abstract: 
  

  Ethylene-insensitive3 (EIN3) and EIN3-like (EIL) proteins are essential transcription factors in the ethylene signaling of higher plants. The EIN3/EIL proteins bind to the promoter regions of the downstream genes and regulate their expression. The location of the DNA-binding domain (DBD) in the primary structure was unclear, since the proteins show no sequence similarity to other known DBDs. Here, we identify the major DBD of an EIN3/EIL protein, Arabidopsis thaliana EIL3, containing a key mutational site for DNA binding and signaling (ein3-3 site), and determine its solution structure by NMR spectroscopy. The structure consists of five alpha-helices, possessing a novel fold dissimilar to known DBD structures. By a chemical-shift perturbation analysis, a region including the ein3-3 site is suggested to be involved in DNA binding.

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Organizational Affiliation: 
• Age Dimension Research Center, 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: 15.65 kDa 
• Atom Count: 1,029 
• Modeled Residue Count: 127 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ETHYLENE-INSENSITIVE3-like 3 protein	A	140	Arabidopsis thaliana	Mutation(s): 0  Gene Names: EIL3
UniProt
Find proteins for O23116 (Arabidopsis thaliana) Explore O23116  Go to UniProtKB:  O23116

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.4: 2024-05-29
  Changes: Data collection