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 

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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 response factor (AP2/ERF) superfamily, is a transcription factor that regulates stress-responsive genes by recognizing a specific cis-acting element of target DNA ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ethylene-responsive transcription factor ERF096A131Arabidopsis thalianaMutation(s): 0 
Gene Names: ERF096At5g43410MWF20.11
UniProt
Find proteins for Q9LSX0 (Arabidopsis thaliana)
Explore Q9LSX0 
Go to UniProtKB:  Q9LSX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LSX0
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
GCC-box motifB11Arabidopsis thaliana
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
GCC-box motifC11Arabidopsis thaliana
Protein Feature View
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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