5WX9

Crystal Structure of AtERF96 with GCC-box


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into Arabidopsis ethylene response factor 96 with an extended N-terminal binding to GCC box.

Chen, C.Y.Lin, P.H.Chen, K.H.Cheng, Y.S.

(2020) Plant Mol Biol 104: 483-498

  • DOI: 10.1007/s11103-020-01052-5
  • Primary Citation of Related Structures:  
    5WX9

  • PubMed Abstract: 
  • The phytohormone ethylene is widely involved in many developmental processes and is a crucial regulator of defense responses against biotic and abiotic stresses in plants. Ethylene-responsive element binding protein, a member of the APETALA2/ethylene ...

    The phytohormone ethylene is widely involved in many developmental processes and is a crucial regulator of defense responses against biotic and abiotic stresses in plants. Ethylene-responsive element binding protein, a member of the APETALA2/ethylene response factor (AP2/ERF) superfamily, is a transcription factor that regulates stress-responsive genes by recognizing a specific cis-acting element of target DNA. A previous study showed only the NMR structure of the AP2/ERF domain of AtERF100 in complex with a GCC box DNA motif. In this report, we determined the crystal structure of AtERF96 in complex with a GCC box at atomic resolution. We analyzed the binding residues of the conserved AP2/ERF domain in the DNA recognition sequence. In addition to the AP2/ERF domain, an N-terminal α-helix of AtERF96 participates in DNA interaction in the flanking region. We also demonstrated the structure of AtERF96 EDLL motif, a unique conserved motif in the group IX of AP2/ERF family, might involve in the transactivation of defense-related genes. Our study establishes the structural basis of the AtERF96 transcription factor in complex with the GCC box, as well as the DNA binding mechanisms of the N-terminal α-helix and AP2/ERF domain.


    Organizational Affiliation

    Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan. chengys@ntu.edu.tw.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ethylene-responsive transcription factor ERF096A131Arabidopsis thalianaMutation(s): 0 
Gene Names: ERF096At5g43410MWF20.11
Find proteins for Q9LSX0 (Arabidopsis thaliana)
Explore Q9LSX0 
Go to UniProtKB:  Q9LSX0
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    GCC-box motifB11Arabidopsis thaliana
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      GCC-box motifC11Arabidopsis thaliana
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.76 Å
      • R-Value Free: 0.225 
      • R-Value Work: 0.206 
      • R-Value Observed: 0.208 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 38.976α = 90
      b = 81.181β = 120.04
      c = 38.999γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data collection
      SCALEPACKdata scaling
      DENZOdata reduction
      PDB_EXTRACTdata extraction
      PHASERphasing
      PHENIXmodel building

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2017-11-22
        Type: Initial release
      • Version 1.1: 2020-11-18
        Changes: Database references