3KMD

Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer.

Chen, Y.Dey, R.Chen, L.

(2010) Structure 18: 246-256

  • DOI: 10.1016/j.str.2009.11.011
  • Primary Citation of Related Structures:  
    3KMD

  • PubMed Abstract: 
  • Recent studies suggest that p53 binds predominantly to consensus sites composed of two decameric half-sites with zero spacing in vivo. Here we report the crystal structure of the p53 core domain bound to a full consensus site as a tetramer at 2.13A r ...

    Recent studies suggest that p53 binds predominantly to consensus sites composed of two decameric half-sites with zero spacing in vivo. Here we report the crystal structure of the p53 core domain bound to a full consensus site as a tetramer at 2.13A resolution. Comparison with previously reported structures of p53 dimer:DNA complexes and a chemically trapped p53 tetramer:DNA complex reveals that DNA binding by the p53 core domain is a cooperative self-assembling process accompanied by structural changes of the p53 dimer and DNA. Each p53 monomer interacts with its two neighboring subunits through two different protein-protein interfaces. The DNA is largely B-form and shows no discernible bend, but the central base-pairs between the two half-sites display a significant slide. The extensive protein-protein and protein-DNA interactions explain the high cooperativity and kinetic stability of p53 binding to contiguous decameric sites and the conservation of such binding-site configuration in vivo.


    Organizational Affiliation

    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular tumor antigen p53ABCD200Homo sapiensMutation(s): 0 
Gene Names: TP53P53
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3'E, F19N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.15 Å
    • R-Value Free: 0.239 
    • R-Value Work: 0.216 
    • R-Value Observed: 0.217 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 65.084α = 90
    b = 93.713β = 90
    c = 145.57γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2010-02-23
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2012-03-21
      Changes: Database references
    • Version 1.3: 2017-11-01
      Changes: Refinement description