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: 124340.09 
• Atom Count: 8524 
• Residue Count: 1000 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

4MZR

Crystal structure of a polypeptide p53 mutant bound to DNA

• DOI: 10.2210/pdb4MZR/pdb
• NDB: NA2742

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2013-09-30 Released: 2014-01-15 
• Deposition Author(s): Emamzadah, S.T., Tropia, L., Vincenti, I., Falquet, B., Halazonetis, T.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.281 
• R-Value Work: 0.234 

Literature

Reversal of the DNA-Binding-Induced Loop L1 Conformational Switch in an Engineered Human p53 Protein.

Emamzadah, S., Tropia, L., Vincenti, I., Falquet, B., Halazonetis, T.D.

(2014) J.Mol.Biol. 426: 936-944

• PubMed: 24374182 
• DOI: 10.1016/j.jmb.2013.12.020
• Primary Citation of Related Structures:  
  4MZI


• PubMed Abstract: 
  

The gene encoding the p53 tumor suppressor protein, a sequence-specific DNA binding transcription factor, is the most frequently mutated gene in human cancer. Crystal structures of homo-oligomerizing p53 polypeptides with specific DNA suggest that DNA binding is associated with a conformational switch. Specifically, in the absence of DNA, loop L1 of the p53 DNA binding domain adopts an extended conformation, whereas two p53 subunits switch to a recessed loop L1 conformation when bound to DNA as a tetramer. We previously designed a p53 protein, p53FG, with amino substitutions S121F and V122G targeting loop L1. These two substitutions enhanced the affinity of p53 for specific DNA yet, counterintuitively, decreased the residency time of p53 on DNA. Here, we confirmed these DNA binding properties of p53FG using a different method. We also determined by crystallography the structure of p53FG in its free state and bound to DNA as a tetramer. In the free state, loop L1 adopted a recessed conformation, whereas upon DNA binding, two subunits switched to the extended loop L1 conformation, resulting in a final structure that was very similar to that of wild-type p53 bound to DNA. Thus, altering the apo structure of p53 changed its DNA binding properties, even though the DNA-bound structure was not altered.

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Organizational Affiliation: 

Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cellular tumor antigen p53	A, B, C, D	237	Homo sapiens	Mutation(s): 2  Gene Names: TP53 (P53)
Find proteins for P04637 (Homo sapiens) Go to Gene View: TP53 Go to UniProtKB:  P04637

Entity ID: 2
Molecule	Chains	Length	Organism
consensus DNA sense strand	K	26	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
consensus DNA anti-sense strand	L	26	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.281 
• R-Value Work: 0.234 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 163.298	α = 90.00
b = 169.764	β = 90.00
c = 55.664	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CNS	phasing
CNS	refinement
MxCuBE	data collection
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-30 
• Released Date: 2014-01-15 
• Deposition Author(s): Emamzadah, S.T., Tropia, L., Vincenti, I., Falquet, B., Halazonetis, T.D.

Revision History 

• Version 1.0: 2014-01-15
  Type: Initial release
• Version 1.1: 2014-02-12
  Type: Database references