3COQ

Structural Basis for Dimerization in DNA Recognition by Gal4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    3COQ

  • 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 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 ...

    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

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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory protein GAL4C [auth A],
D [auth B]		89Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GAL4
UniProt
Find proteins for P04386 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04386 
Go to UniProtKB:  P04386
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04386
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')A [auth D]20synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')B [auth E]20synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
Download Ideal Coordinates CCD File 
E [auth D](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth B],
I [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.495α = 90
b = 40.829β = 95.88
c = 90.418γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
SOLVEphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description, Source and taxonomy