Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.47 kDa 
• Atom Count: 3792 
• Residue Count: 420 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2ADY

Structural Basis of DNA Recognition by p53 Tetramers (complex IV)

• DOI: 10.2210/pdb2ADY/pdb
• NDB: PD0694

• Classification: APOPTOSIS/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-07-21 Released: 2006-07-11 
• Deposition Author(s): Kitayner, M., Rozenberg, H., Kessler, N., Rabinovich, D., Shakked, Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.251 
• R-Value Work: 0.164 
• R-Value Observed: 0.169 

Literature

Structural Basis of DNA Recognition by p53 Tetramers

Kitayner, M., Rozenberg, H., Kessler, N., Rabinovich, D., Shaulov, L., Haran, T.E., Shakked, Z.

(2006) Mol Cell 22: 741-753

• PubMed: 16793544 
• DOI: 10.1016/j.molcel.2006.05.015
• Primary Citation of Related Structures:  
  2AC0, 2ATA, 2ADY, 2AHI


• PubMed Abstract: 
  

The tumor-suppressor protein p53 is among the most effective of the cell's natural defenses against cancer. In response to cellular stress, p53 binds as a tetramer to diverse DNA targets containing two decameric half-sites, thereby activating the expression of genes involved in cell-cycle arrest or apoptosis. Here we present high-resolution crystal structures of sequence-specific complexes between the core domain of human p53 and different DNA half-sites. In all structures, four p53 molecules self-assemble on two DNA half-sites to form a tetramer that is a dimer of dimers, stabilized by protein-protein and base-stacking interactions. The protein-DNA interface varies as a function of the specific base sequence in correlation with the measured binding affinities of the complexes. The new data establish a structural framework for understanding the mechanisms of specificity, affinity, and cooperativity of DNA binding by p53 and suggest a model for its regulation by regions outside the sequence-specific DNA binding domain.

---

Organizational Affiliation: 

Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A, B	200	Homo sapiens	Mutation(s): 0  Gene Names: TP53, P53
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637 GTEx  ENSG00000141510

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'	E, F	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.251 
• R-Value Work: 0.164 
• R-Value Observed: 0.169 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.997	α = 90
b = 67.903	β = 92.97
c = 74.989	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-21 
• Released Date: 2006-07-11 
Deposition Author(s): Kitayner, M., Rozenberg, H., Kessler, N., Rabinovich, D., Shakked, Z.

Revision History 

• Version 1.0: 2006-07-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance