3DFX

Opposite GATA DNA binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA.

Bates, D.L.Chen, Y.Kim, G.Guo, L.Chen, L.

(2008) J.Mol.Biol. 381: 1292-1306

  • DOI: 10.1016/j.jmb.2008.06.072
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The GATA family of transcription factors (GATA1-6) binds selected GATA sites in vertebrate genomes to regulate specific gene expression. Although vertebrate GATA factors have two highly conserved zinc finger motifs, how the two fingers act together t ...

    The GATA family of transcription factors (GATA1-6) binds selected GATA sites in vertebrate genomes to regulate specific gene expression. Although vertebrate GATA factors have two highly conserved zinc finger motifs, how the two fingers act together to recognize functional DNA elements is not well understood. Here we determined the crystal structures of the C-terminal zinc finger of mouse GATA3 bound to DNA containing two variously arranged GATA binding sites. Our structures and accompanying biochemical analyses reveal two distinct modes of DNA binding by GATA to closely arranged sites. One mode involves cooperative binding by two GATA factors that interact with each other through protein-protein interactions. The other involves simultaneous binding of the N-terminal zinc finger (N-finger) and the C-terminal zinc finger of the same GATA factor. Our studies represent the first crystallographic analysis of GATA zinc fingers bound to DNA and provide new insights into the DNA recognition mechanism by the GATA zinc finger. Our crystal structure also reveals a dimerization interface in GATA that has previously been shown to be important for GATA self-association. These findings significantly advance our understanding of the structure and function of GATA and provide an important framework for further investigating the in vivo mechanisms of GATA-dependent gene regulation.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Trans-acting T-cell-specific transcription factor GATA-3
A, B
63Mus musculusMutation(s): 0 
Gene Names: Gata3 (Gata-3)
Find proteins for P23772 (Mus musculus)
Go to UniProtKB:  P23772
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3')X20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3')Y20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.276 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.882α = 90.00
b = 30.370β = 93.82
c = 75.648γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description