Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 24.68 kDa 
• Atom Count: 1583 
• Modelled Residue Count: 183 
• Deposited Residue Count: 219 
• Unique protein chains: 1

2BIN

human p53 core domain mutant M133L-H168R-V203A-N239Y-N268D

• DOI: 10.2210/pdb2BIN/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-01-25 Released: 2005-01-26 
• Deposition Author(s): Joerger, A.C., Fersht, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Structures of P53 Cancer Mutants and Mechanism of Rescue by Second-Site Suppressor Mutations

Joerger, A.C., Ang, H.C., Veprintsev, D.B., Blair, C.M., Fersht, A.R.

(2005) J Biol Chem 280: 16030

• PubMed: 15703170 
• DOI: 10.1074/jbc.M500179200
• Primary Citation of Related Structures:  
  2BIP, 2BIO, 2BIN, 2BIM, 2BIQ


• PubMed Abstract: 
  

We have solved the crystal structures of three oncogenic mutants of the core domain of the human tumor suppressor p53. The mutations were introduced into a stabilized variant. The cancer hot spot mutation R273H simply removes an arginine involved in DNA binding without causing structural distortions in neighboring residues. In contrast, the "structural" oncogenic mutations H168R and R249S induce substantial structural perturbation around the mutation site in the L2 and L3 loops, respectively. H168R is a specific intragenic suppressor mutation for R249S. When both cancer mutations are combined in the same molecule, Arg(168) mimics the role of Arg(249) in wild type, and the wild type conformation is largely restored in both loops. Our structural and biophysical data provide compelling evidence for the mechanism of rescue of mutant p53 by intragenic suppressor mutations and reveal features by which proteins can adapt to deleterious mutations.

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Related Citations: 

• Crystal Structure of a Superstable Mutant of Human P53 Core Domain: Insights Into the Mechanism of Rescuing Oncogenic Mutations
  Joerger, A.C., Allen, M.D., Fersht, A.R.
  (2004) J Biol Chem 279: 1291

• Crystal Structure of a P53 Tumor Suppressor-DNA Complex: Understanding Tumorigenic Mutations
  Cho, Y., Gorina, S., Jeffrey, P.D., Pavletich, N.P.
  (1994) Science 265: 346

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Organizational Affiliation: 

Centre for Protein Engineering, Medical Research Council, Cambridge, CB2 2QH, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLULAR TUMOR ANTIGEN P53	A	219	Homo sapiens	Mutation(s): 4  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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.045	α = 90
b = 45.045	β = 90
c = 331.78	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-25 
• Released Date: 2005-01-26 
Deposition Author(s): Joerger, A.C., Fersht, A.R.

Revision History  

• Version 1.0: 2005-01-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance