1B3T

EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2.2 A structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1.

Bochkarev, A.Bochkareva, E.Frappier, L.Edwards, A.M.

(1998) J.Mol.Biol. 284: 1273-1278

  • DOI: 10.1006/jmbi.1998.2247

  • PubMed Abstract: 
  • Epstein-Barr nuclear antigen 1 (EBNA1) binds to four recognition sites in the minimal origin of latent DNA replication of Epstein-Barr virus and activates latent-phase replication of the viral genomes. Two of these EBNA1 binding sites become sensitiv ...

    Epstein-Barr nuclear antigen 1 (EBNA1) binds to four recognition sites in the minimal origin of latent DNA replication of Epstein-Barr virus and activates latent-phase replication of the viral genomes. Two of these EBNA1 binding sites become sensitive to permanganate oxidation when bound by the DNA binding and dimerization domains of EBNA1. We have previously solved the co-crystal structure of this EBNA1 fragment bound to a consensus recognition site that is not sensitive to permanganate oxidation (CS). To understand the structural difference that underlies the permanganate sensitivity of EBNA1 binding sites, we have now solved the crystal structure of the EBNA1 DNA-binding and dimerization domains bound to a permanganate-sensitive site (CSA/T). Comparisons of permanganate-sensitive and insensitive EBNA1-DNA complexes have revealed only minor differences in protein and DNA structures. In the EBNA1-CSA/T structure, interstrand H-bonds for three consecutive base-pairs centered over the permanganate-sensitive thymine base are lengthened relative to the corresponding bonds in the EBNA1-CS complex, and three potential intrastrand H-bonds were observed between adjacent bases. We also observed that both the CS and CSA/T sequences are overwound by EBNA1 in the vicinity of the permanganate-sensitive thymine base. Finally, we show that the permanganate-sensitive thymine base in the CSA/T-EBNA1 complex is more accessible to solvent than the corresponding T in the EBNA-CS complex.


    Related Citations: 
    • Crystal Structure of the DNA-Binding Domain of Theepstein-Barr Virus Origin- Binding Protein, EBNA1, Boundto DNA
      Bochkarev, A.,Barwell, J.A.,Pfuetzner, R.A.,Bochkareva, E.,Frappier, L.,Edwards, A.M.
      (1996) Cell 84: 791
    • Overexpression, Purification, and Crystallization of the DNA Binding and Dimerization Domains of the Epstein-Barr Virus Nuclear Antigen 1
      Barwell, J.A.,Bochkarev, A.,Pfuetzner, R.A.,Tong, H.,Yang, D.S.,Frappier, L.,Edwards, A.M.
      (1995) J.Biol.Chem. 270: 20556


    Organizational Affiliation

    Department of Medical Genetics and Microbiology, University of Toronto, 1 Kings College Circle, Toronto, Ontario, M5S 1A8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (NUCLEAR PROTEIN EBNA1)
A, B
147Epstein-Barr virus (strain B95-8)Gene Names: EBNA1
Find proteins for P03211 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P03211
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*AP*TP*AP*TP*GP*CP*TP*TP*CP*CP*C)-3')C,D18N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.083α = 90.00
b = 64.501β = 90.00
c = 111.938γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-15
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance