3US1

Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair Response Element Containing a Two Base Pair "GC" Spacer Between Half Sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63.

Chen, C.Gorlatova, N.Herzberg, O.

(2012) J.Biol.Chem. 287: 7477-7486

  • DOI: 10.1074/jbc.M111.315820
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We show that changes in the nucleotide sequence alter the DNA conformation in the crystal structures of p63 DNA-binding domain (p63DBD) bound to its response element. The conformation of a 22-bp canonical response element containing an AT spacer betw ...

    We show that changes in the nucleotide sequence alter the DNA conformation in the crystal structures of p63 DNA-binding domain (p63DBD) bound to its response element. The conformation of a 22-bp canonical response element containing an AT spacer between the two half-sites is unaltered compared with that containing a TA spacer, exhibiting superhelical trajectory. In contrast, a GC spacers abolishes the DNA superhelical trajectory and exhibits less bent DNA, suggesting that increased GC content accompanies increased double helix rigidity. A 19-bp DNA, representing an AT-rich response element with overlapping half-sites, maintains superhelical trajectory and reveals two interacting p63DBD dimers crossing one another at 120°. p63DBD binding assays to response elements of increasing length complement the structural studies. We propose that DNA deformation may affect promoter activity, that the ability of p63DBD to bind to superhelical DNA suggests that it is capable of binding to nucleosomes, and that overlapping response elements may provide a mechanism to distinguish between p63 and p53 promoters.


    Organizational Affiliation

    W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research and the Department of Chemistry and Biochemistry, University of Maryland, Rockville, Maryland 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor protein 63
A, D
203Homo sapiensMutation(s): 0 
Gene Names: TP63 (KET, P63, P73H, P73L, TP73L)
Find proteins for Q9H3D4 (Homo sapiens)
Go to Gene View: TP63
Go to UniProtKB:  Q9H3D4
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*GP*CP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'F22N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.954α = 90.00
b = 101.220β = 122.78
c = 71.501γ = 90.00
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
XDSdata reduction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-11-22 
  • Released Date: 2012-02-01 
  • Deposition Author(s): Chen, C., Herzberg, O.

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-03-21
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description