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: 122.71 kDa 
• Atom Count: 8677 
• Residue Count: 988 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

3Q05

An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity

• DOI: 10.2210/pdb3Q05/pdb
• NDB: NA0885

• Classification: ANTITUMOR PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-12-15 Released: 2011-05-11 
• Deposition Author(s): Petty, T.J., Halazonetis, T.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.267 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity.

Petty, T.J., Emamzadah, S., Costantino, L., Petkova, I., Stavridi, E.S., Saven, J.G., Vauthey, E., Halazonetis, T.D.

(2011) EMBO J 30: 2167-2176

• PubMed: 21522129 
• DOI: 10.1038/emboj.2011.127
• Primary Citation of Related Structures:  
  3Q01, 3Q05, 3Q06


• PubMed Abstract: 
  

The p53 tumour suppressor gene, the most frequently mutated gene in human cancer, encodes a transcription factor that contains sequence-specific DNA binding and homo-tetramerization domains. Interestingly, the affinities of p53 for specific and non-specific DNA sites differ by only one order of magnitude, making it hard to understand how this protein recognizes its specific DNA targets in vivo. We describe here the structure of a p53 polypeptide containing both the DNA binding and oligomerization domains in complex with DNA. The structure reveals that sequence-specific DNA binding proceeds via an induced fit mechanism that involves a conformational switch in loop L1 of the p53 DNA binding domain. Analysis of loop L1 mutants demonstrated that the conformational switch allows DNA binding off-rates to be regulated independently of affinities. These results may explain the universal prevalence of conformational switching in sequence-specific DNA binding proteins and suggest that proteins like p53 rely more on differences in binding off-rates, than on differences in affinities, to recognize their specific DNA sites.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A, B, C, D	234	Homo sapiens	Mutation(s): 18  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: 2
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	K	26	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	L	26	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.267 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.298	α = 90
b = 169.764	β = 90
c = 55.664	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-15 
• Released Date: 2011-05-11 
Deposition Author(s): Petty, T.J., Halazonetis, T.D.

Revision History 

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-24
  Changes: Other
• Version 1.3: 2017-07-26
  Changes: Refinement description, Source and taxonomy