1P47

Crystal Structure of tandem Zif268 molecules complexed to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Constraints for Zinc Finger Linker Design as Inferred from X-ray Crystal Structure of Tandem Zif268-DNA Complexes

Peisach, E.Pabo, C.O.

(2003) J.Mol.Biol. 330: 1-7


  • PubMed Abstract: 
  • Zinc-finger proteins offer a versatile and effective framework for the recognition of DNA binding sites. By connecting multiple fingers together with canonical TGEKP linkers, a protein may be designed to recognize almost any desired target DNA sequen ...

    Zinc-finger proteins offer a versatile and effective framework for the recognition of DNA binding sites. By connecting multiple fingers together with canonical TGEKP linkers, a protein may be designed to recognize almost any desired target DNA sequence. However, proteins containing more than three zinc-fingers do not bind as tightly as one might predict, and it appears that some type of strain is introduced when a six-finger protein is constructed with canonical linkers. In an attempt to understand the sources of this strain, we have solved the 2.2A resolution X-ray crystallographic structure of a complex that has two copies of the three-finger Zif268 protein bound to adjacent sites on one duplex DNA. Conceptually, this is equivalent to a six-finger protein in which the central linker has been removed and the complex has been allowed to "relax" to its most stable conformation. As in other Zif268-DNA complexes, the DNA is approximately linear and is slightly underwound. Surprisingly, the structure of the complex is similar (within 0.5A) to an arrangement that would allow a canonical linker at the center of the complex, and it seems possible that entropic effects (involving the librational degrees of freedom in the complex) could be important in determining optimal linker length.


    Related Citations: 
    • Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants.
      Kim, J.S.,Pabo, C.O.
      (1998) Proc.Natl.Acad.Sci.USA 95: 2812
    • Zif268 protein-DNA complex refined at 1.6A: implications for understanding zinc finger DNA recognition
      Elrod-Erickson, M.,Rould, M.A.,Nekludova, L.,Pabo, C.O.
      (1996) Structure 6: 451


    Organizational Affiliation

    Department of Biology, Howard Hughes Medical Institute, Cambridge, MA, USA. epeisach@med-xtal.bu.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Early growth response protein 1
A, B
87Mus musculusGene Names: Egr1 (Egr-1, Krox-24)
Find proteins for P08046 (Mus musculus)
Go to UniProtKB:  P08046
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3'C22N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*A)-3'D22N/A
Small Molecules
Ligands 1 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 2.1E-6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 70.629α = 90.00
b = 70.629β = 90.00
c = 99.608γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance