3COQ

Structural Basis for Dimerization in DNA Recognition by Gal4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for dimerization in DNA recognition by gal4.

Hong, M.Fitzgerald, M.X.Harper, S.Luo, C.Speicher, D.W.Marmorstein, R.

(2008) Structure 16: 1019-1026

  • DOI: 10.1016/j.str.2008.03.015

  • PubMed Abstract: 
  • Gal4 is a Zn2Cys6 binuclear cluster containing transcription factor that binds DNA as a homodimer and can activate transcription by interacting with the mutant Gal11P protein. Although structures have been reported of the Gal4 dimerization domain and ...

    Gal4 is a Zn2Cys6 binuclear cluster containing transcription factor that binds DNA as a homodimer and can activate transcription by interacting with the mutant Gal11P protein. Although structures have been reported of the Gal4 dimerization domain and the binuclear cluster domain bound to DNA as a dimer, the structure of the "complete" Gal4 dimer bound to DNA has not previously been described. Here we report the structure of a complete Gal4 dimer bound to DNA and additional biochemical studies to address the molecular basis for Gal4 dimerization in DNA binding. We find that Gal4 dimerization on DNA is mediated by an intertwined helical bundle that deviates significantly from the solution NMR structure of the free dimerization domain. Associated biochemical studies show that the dimerization domain of Gal4 is important for DNA binding and protein thermostability. We also map the interaction surface of the Gal4 dimerization domain with Gal11P.


    Organizational Affiliation

    The Wistar Institute, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Regulatory protein GAL4
A, B
89Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GAL4
Find proteins for P04386 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04386
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')D20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')E20N/A
Small Molecules
Ligands 2 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
MPD
Query on MPD

Download SDF File 
Download CCD File 
D
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 126.495α = 90.00
b = 40.829β = 95.88
c = 90.418γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
HKL-2000data collection
CNSphasing
CNSrefinement
SOLVEphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description