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 

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

  • 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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellular tumor antigen p53
A, B, D, C
200Homo sapiensMutation(s): 0 
Gene Names: TP53 (P53)
Find proteins for P04637 (Homo sapiens)
Go to Gene View: TP53
Go to UniProtKB:  P04637
Entity ID: 2
MoleculeChainsLengthOrganism
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 SDF File 
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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.084α = 90.00
b = 93.713β = 90.00
c = 145.570γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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