1LLM

Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 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
  • Primary Citation of Related Structures:  
    1LLM

  • 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 finger protein has been created that binds cooperatively to DNA via an attached leucine zipper dimerization domain ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
chimera of Zif23-GCN4C, D88Mus musculusSaccharomyces cerevisiae
This entity is chimeric
Mutation(s): 0 
Gene Names: Egr1
UniProt & NIH Common Fund Data Resources
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03069 
Go to UniProtKB:  P03069
Find proteins for P08046 (Mus musculus)
Explore P08046 
Go to UniProtKB:  P08046
IMPC:  MGI:95295
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3'A, B13N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.50 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
    b = 87.398β = 90
    c = 118.693γ = 120
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    X-PLORmodel building
    X-PLORrefinement
    X-PLORphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

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