1F2I

COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selected peptide extension contacts hydrophobic patch on neighboring zinc finger and mediates dimerization on DNA.

Wang, B.S.Grant, R.A.Pabo, C.O.

(2001) Nat.Struct.Mol.Biol. 8: 589-593

  • DOI: 10.1038/89617

  • PubMed Abstract: 
  • Protein-protein interactions often play a crucial role in stabilizing protein-DNA complexes and thus facilitate site-specific DNA recognition. We have worked to incorporate such protein-protein contacts into our design and selection strategies for sh ...

    Protein-protein interactions often play a crucial role in stabilizing protein-DNA complexes and thus facilitate site-specific DNA recognition. We have worked to incorporate such protein-protein contacts into our design and selection strategies for short peptide extensions that promote cooperative binding of zinc finger proteins to DNA. We have determined the crystal structure of one of these fusion protein-DNA complexes. The selected peptide extension was found to mediate dimerization by reaching across the dyad axis and contacting a hydrophobic patch on the surface of the zinc finger bound to the adjacent DNA site. The peptide-zinc finger protein interactions observed in this structure are similar to those of some homeodomain heterodimers. We also find that the region of the zinc finger surface contacted by the selected peptide extension corresponds to surfaces that also make key interactions in the zinc finger proteins GLI and SWI5.


    Related Citations: 
    • Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences
      Wang, B.S.,Pabo, C.O.
      (1999) Proc.Natl.Acad.Sci.USA 96: 9568


    Organizational Affiliation

    [1] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
G, H, I, J, K, L
73Mus musculusGene Names: Egr1 (Egr-1, Krox-24)
Find proteins for P08046 (Mus musculus)
Go to UniProtKB:  P08046
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'A,B,C,D,E,F14N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
G, H, I, J, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 86.300α = 90.00
b = 86.300β = 90.00
c = 133.000γ = 120.00
Software Package:
Software NamePurpose
DMmodel building
X-PLORrefinement
DENZOdata reduction
DMphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance