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

  • Resolution: 2.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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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: https://doi.org/10.1074/jbc.M111.315820
  • Primary Citation of Related Structures:  
    3US0, 3US1, 3US2

  • 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 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.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor protein 63A,
B [auth D]
203Homo sapiensMutation(s): 0 
Gene Names: KETP63P73HP73LTP63TP73L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3D4 (Homo sapiens)
Explore Q9H3D4 
Go to UniProtKB:  Q9H3D4
GTEx:  ENSG00000073282 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3D4
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.954α = 90
b = 101.22β = 122.78
c = 71.501γ = 90
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description