3EXL

Crystal Structure of a p53 Core Tetramer Bound to DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of a p53 core tetramer bound to DNA.

Malecka, K.A., Ho, W.C., Marmorstein, R.

(2009) Oncogene 28: 325-333

  • DOI: 10.1038/onc.2008.400
  • Primary Citation of Related Structures:  
    3EXJ, 3EXL

  • PubMed Abstract: 

    • The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA ...

    The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

    Organizational Affiliation: 

    The Wistar Institute, Philadelphia, PA 19104, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mouse p53 core domainA197Mus musculusMutation(s): 0 
Gene Names: Tp53, P53, Trp53
Find proteins for P02340 (Mus musculus)
Explore P02340 
Go to UniProtKB:  P02340
NIH Common Fund Data Resources
IMPC  MGI:98834
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'C11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'D12N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      FLC
      Query on FLC
      Download Ideal Coordinates CCD File 
      A
      		CITRATE ANION
      C6 H5 O7
      KRKNYBCHXYNGOX-UHFFFAOYSA-K      		 Ligand Interaction
      ZN
      Query on ZN
      Download Ideal Coordinates CCD File 
      A
      		ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.20 Å
      • R-Value Free: 0.253 
      • R-Value Work: 0.202 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 109.418α = 90
      b = 68.103β = 104.18
      c = 34.428γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      PDB_EXTRACTdata extraction
      Blu-Icedata collection
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      • Deposited Date: 2008-10-16 
      • Released Date: 2008-12-16 
        • Deposition Author(s): Malecka, K.A.

      Revision History 

      • Version 1.0: 2008-12-16
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2017-10-25
        Changes: Refinement description