4F2J

Crystal structure of ZNF217 bound to DNA, P6522 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217

Vandevenne, M.S.Jacques, D.A.Artuz, C.Nguyen, C.D.Kwan, A.H.Segal, D.J.Matthews, J.M.Crossley, M.Guss, J.M.Mackay, J.P.

(2013) J.Biol.Chem. 288: 10616-10627

  • DOI: 10.1074/jbc.M112.441451

  • PubMed Abstract: 
  • Classical zinc fingers (ZFs) are one of the most abundant and best characterized DNA-binding domains. Typically, tandem arrays of three or more ZFs bind DNA target sequences with high affinity and specificity, and the mode of DNA recognition is suffi ...

    Classical zinc fingers (ZFs) are one of the most abundant and best characterized DNA-binding domains. Typically, tandem arrays of three or more ZFs bind DNA target sequences with high affinity and specificity, and the mode of DNA recognition is sufficiently well understood that tailor-made ZF-based DNA-binding proteins can be engineered. We have shown previously that a two-zinc finger unit found in the transcriptional coregulator ZNF217 recognizes DNA but with an affinity and specificity that is lower than other ZF arrays. To investigate the basis for these differences, we determined the structure of a ZNF217-DNA complex. We show that although the overall position of the ZFs on the DNA closely resembles that observed for other ZFs, the side-chain interaction pattern differs substantially from the canonical model. The structure also reveals the presence of two methyl-π interactions, each featuring a tyrosine contacting a thymine methyl group. To our knowledge, interactions of this type have not previously been described in classical ZF-DNA complexes. Finally, we investigated the sequence specificity of this two-ZF unit and discuss how ZNF217 might discriminate its target DNA sites in the cell.


    Organizational Affiliation

    School of Molecular Bioscience, University of Sydney, New South Wales, 2006 Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Zinc finger protein 217
C
57Homo sapiensMutation(s): 0 
Gene Names: ZNF217 (ZABC1)
Find proteins for O75362 (Homo sapiens)
Go to Gene View: ZNF217
Go to UniProtKB:  O75362
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'A20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.252 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.928α = 90.00
b = 56.928β = 90.00
c = 242.542γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
MAR345dtbdata collection
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references