Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.07 kDa 
• Atom Count: 1,791 
• Modelled Residue Count: 153 
• Deposited Residue Count: 153 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 5WX9

Crystal Structure of AtERF96 with GCC-box

• PDB DOI: 10.2210/pdb5WX9/pdb
• NDB: 5WX9

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3), synthetic construct
• Mutation(s): No 


• Deposited: 2017-01-06 Released: 2017-11-22 
• Deposition Author(s): Chen, C.Y., Cheng, Y.S.

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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 

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

• PubMed: 32813232 
• 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. 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.

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Organizational Affiliation: 

Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethylene-responsive transcription factor ERF096	A	131	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ERF096, At5g43410, MWF20.11
UniProt
Find proteins for Q9LSX0 (Arabidopsis thaliana) Explore Q9LSX0  Go to UniProtKB:  Q9LSX0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
GCC-box motif	B	11	Arabidopsis thaliana

Entity ID: 3
Molecule	Chains	Length	Organism	Image
GCC-box motif	C	11	Arabidopsis 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 = 38.976	α = 90
b = 81.181	β = 120.04
c = 38.999	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
SCALEPACK	data scaling
DENZO	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Chen, C.Y., Cheng, Y.S.

Revision History  

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