1LLM

Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a designed dimeric zinc finger protein bound to DNA.

Wolfe, S.A.Grant, R.A.Pabo, C.O.

(2003) Biochemistry 42: 13401-13409

  • DOI: 10.1021/bi034830b

  • PubMed Abstract: 
  • Proteins that employ dimerization domains to bind cooperatively to DNA have a number of potential advantages over monomers with regards to gene regulation. Using a combination of structure-based design and phage display, a dimeric Cys(2)His(2) zinc f ...

    Proteins that employ dimerization domains to bind cooperatively to DNA have a number of potential advantages over monomers with regards to gene regulation. Using a combination of structure-based design and phage display, a dimeric Cys(2)His(2) zinc finger protein has been created that binds cooperatively to DNA via an attached leucine zipper dimerization domain. This chimera, derived from components of Zif268 and GCN4, displayed excellent DNA-binding specificity, and we now report the 1.5 A resolution cocrystal structure of the Zif268-GCN4 homodimer bound to DNA. This structure shows how phage display has annealed the DNA binding and dimerization domains into a single functional unit. Moreover, this chimera provides a potential platform for the creation heterodimeric zinc finger proteins that can regulate a desired target gene through cooperative DNA recognition.


    Related Citations: 
    • Combining Structure-based Design with Phage Display to Create New Cys(2)His(2) Zinc Finger Dimers
      Wolfe, S.A.,Ramm, E.I.,Pabo, C.O.
      (2000) Structure 8: 739


    Organizational Affiliation

    Department of Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. scot.wolfe@umassmed.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
chimera of Zif23-GCN4
C, D
88Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mus musculus
This entity is chimeric
Gene Names: GCN4 (AAS3, ARG9), Egr1 (Egr-1, Krox-24)
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P03069
Find proteins for P08046 (Mus musculus)
Go to UniProtKB:  P08046
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3'A,B13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.398α = 90.00
b = 87.398β = 90.00
c = 118.693γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
SCALEPACKdata scaling
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-16
    Type: Refinement description, Source and taxonomy