1P47

Crystal Structure of tandem Zif268 molecules complexed to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.219 

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

  • DOI: 10.1016/s0022-2836(03)00572-2
  • Primary Citation of Related Structures:  
    1P47

  • 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 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 ...

    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: 
    • 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
    • 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 U S A 95: 2812

    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Early growth response protein 1C [auth A], D [auth B]87Mus musculusMutation(s): 0 
Gene Names: EGR1 OR EGR-1 OR KROX-24Egr1Egr-1Krox-24
UniProt & NIH Common Fund Data Resources
Find proteins for P08046 (Mus musculus)
Explore P08046 
Go to UniProtKB:  P08046
IMPC:  MGI:95295
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
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'A [auth C]22N/A
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
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'B [auth D]22N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  1P47 Kd: 2.10e-6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.219 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.629α = 90
b = 70.629β = 90
c = 99.608γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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