Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29649.67 
• Atom Count: 1736 
• Residue Count: 220 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

3EXL

Crystal Structure of a p53 Core Tetramer Bound to DNA

• DOI: 10.2210/pdb3EXL/pdb
• NDB: PD1192

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli


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

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Experimental Data Snapshot

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

Literature

Crystal structure of a p53 core tetramer bound to DNA.

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

(2009) Oncogene 28: 325-333

• PubMed: 18978813 
• DOI: 10.1038/onc.2008.400
• Primary Citation of Related Structures:  
  3EXJ


• 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 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.

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Organizational Affiliation: 

The Wistar Institute, Philadelphia, PA 19104, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
mouse p53 core domain	A	197	Mus musculus	Mutation(s): 0  Gene Names: Tp53 (P53, Trp53)
Find proteins for P02340 (Mus musculus) Go to UniProtKB:  P02340

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'	C	11	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'	D	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FLC	A	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

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 = 109.418	α = 90.00
b = 68.103	β = 104.18
c = 34.428	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction

Structure Validation

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