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 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 Biol 8: 589-593

  • DOI: https://doi.org/10.1038/89617
  • Primary Citation of Related Structures:  
    1F2I

  • 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 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.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FUSION OF N-TERMINAL 17-MER PEPTIDE EXTENSION TO ZIF12
G, H, I, J, K
G, H, I, J, K, L
73Mus musculusMutation(s): 0 
Gene Names: GENE FOR ZIF12
UniProt & NIH Common Fund Data Resources
Find proteins for P08046 (Mus musculus)
Explore P08046 
Go to UniProtKB:  P08046
IMPC:  MGI:95295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08046
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3'
A, B, C, D, E
A, B, C, D, E, F
14N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth G]
N [auth G]
O [auth H]
P [auth H]
Q [auth I]
M [auth G],
N [auth G],
O [auth H],
P [auth H],
Q [auth I],
R [auth I],
S [auth J],
T [auth J],
U [auth K],
V [auth K],
W [auth L],
X [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.215 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.3α = 90
b = 86.3β = 90
c = 133γ = 120
Software Package:
Software NamePurpose
DMmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations