3EXL

Crystal Structure of a p53 Core Tetramer Bound to DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


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:  

  • 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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mouse p53 core domain
A
197Mus musculusMutation(s): 0 
Gene Names: Tp53 (P53, Trp53)
Find proteins for P02340 (Mus musculus)
Go to UniProtKB:  P02340
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'C11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC
Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 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 = 90.00
b = 68.103β = 104.18
c = 34.428γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
Blu-Icedata collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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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
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description