Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.60 kDa 
• Atom Count: 1221 
• Modelled Residue Count: 141 
• Deposited Residue Count: 151 
• Unique protein chains: 2

2B3G

p53N (fragment 33-60) bound to RPA70N

• PDB DOI: 10.2210/pdb2B3G/pdb

• Classification: REPLICATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-20 Released: 2005-10-11 
• Deposition Author(s): Bochkareva, E., Kaustov, L., Ayed, A., Yi, G.S., Lu, Y., Pineda-Lucena, A., Liao, J.C., Okorokov, A.L., Milner, J., Arrowsmith, C.H., Bochkarev, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.239 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Literature

Single-stranded DNA mimicry in the p53 transactivation domain interaction with replication protein A.

Bochkareva, E., Kaustov, L., Ayed, A., Yi, G.S., Lu, Y., Pineda-Lucena, A., Liao, J.C., Okorokov, A.L., Milner, J., Arrowsmith, C.H., Bochkarev, A.

(2005) Proc Natl Acad Sci U S A 102: 15412-15417

• PubMed: 16234232 
• DOI: 10.1073/pnas.0504614102
• Primary Citation of Related Structures:  
  2B29, 2B3G


• PubMed Abstract: 
  

One of many protein-protein interactions modulated upon DNA damage is that of the single-stranded DNA-binding protein, replication protein A (RPA), with the p53 tumor suppressor. Here we report the crystal structure of RPA residues 1-120 (RPA70N) bound to the N-terminal transactivation domain of p53 (residues 37-57; p53N) and, by using NMR spectroscopy, characterize two mechanisms by which the RPA/p53 interaction can be modulated. RPA70N forms an oligonucleotide/oligosaccharide-binding fold, similar to that previously observed for the ssDNA-binding domains of RPA. In contrast, the N-terminal p53 transactivation domain is largely disordered in solution, but residues 37-57 fold into two amphipathic helices, H1 and H2, upon binding with RPA70N. The H2 helix of p53 structurally mimics the binding of ssDNA to the oligonucleotide/oligosaccharide-binding fold. NMR experiments confirmed that both ssDNA and an acidic peptide mimicking a phosphorylated form of RPA32N can independently compete the acidic p53N out of the binding site. Taken together, our data suggest a mechanism for DNA damage signaling that can explain a threshold response to DNA damage.

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Organizational Affiliation: 

Banting and Best Department of Medical Research & Department of Medical Genetics and Microbiology, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 70 kDa DNA-binding subunit	A	123	Homo sapiens	Mutation(s): 0  Gene Names: RPA1, REPA1, RPA70
UniProt & NIH Common Fund Data Resources
Find proteins for P27694 (Homo sapiens) Explore P27694  Go to UniProtKB:  P27694
PHAROS:  P27694

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	B	28	Homo sapiens	Mutation(s): 0  Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.239 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.46	α = 90
b = 50.38	β = 90
c = 52.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-20 
• Released Date: 2005-10-11 
Deposition Author(s): Bochkareva, E., Kaustov, L., Ayed, A., Yi, G.S., Lu, Y., Pineda-Lucena, A., Liao, J.C., Okorokov, A.L., Milner, J., Arrowsmith, C.H., Bochkarev, A.

Revision History  

• Version 1.0: 2005-10-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance