6PW2

Structural Basis for Cooperative Binding of EBNA1 to the Epstein-Barr Virus Dyad Symmetry Minimal Origin of Replication


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Cooperative Binding of EBNA1 to the Epstein-Barr Virus Dyad Symmetry Minimal Origin of Replication.

Malecka, K.A.Dheekollu, J.Deakyne, J.S.Wiedmer, A.Ramirez, U.D.Lieberman, P.M.Messick, T.E.

(2019) J.Virol. 93: --

  • DOI: 10.1128/JVI.00487-19

  • PubMed Abstract: 
  • Epstein-Barr virus is associated with several human malignancies including nasopharyngeal carcinoma, gastric cancer and lymphoma. Latently infected cells carry a circularized EBV episome where the origin of replication ( <i>OriP </i>) is comprised of ...

    Epstein-Barr virus is associated with several human malignancies including nasopharyngeal carcinoma, gastric cancer and lymphoma. Latently infected cells carry a circularized EBV episome where the origin of replication ( OriP ) is comprised of two elements: the family of repeats (FR) and dyad symmetry (DS). The viral protein Epstein-Barr Nuclear Antigen-1 (EBNA1) binds to FR and DS to promote EBV episome maintenance and DNA replication during latent infection in proliferating cells. EBNA1 binding to the DS constitutes a minimal origin of DNA replication. Here, we report the crystal structure of two EBNA1 DNA-binding domain dimers bound to a DS half site. This structure shows that the DNA is smoothly bent allowing for stabilizing interactions between the dimers. The dimer-dimer interface requires an intricate hydrogen bonding network involving residues R491 and D581. When this interface is disrupted, we note loss of stable dimer-dimer complex formation on the DNA, compromised OriP -containing plasmid replication in cells and impaired recruitment of the MCM3 complex to the OriP Surface conservation analysis reveals that these residues are part of a larger conserved surface that may be critical for recruitment of replication machinery to the OriP Our results reveal a new region of EBNA1 critical for its activity and one that may be exploited by targeted small molecules to treat EBV-associated disease. IMPORTANCE Epstein-Barr Virus (EBV) is a causative agent of various malignancies and may also contribute to autoimmune disease. The latent and episomal form of the virus is known to drive EBV-associated oncogenesis. Persistence of the viral episome in proliferating tumor cells requires the interaction of the Epstein-Barr Virus Nuclear Antigen 1 (EBNA1) with the viral origin of plasmid replication OriP. The Dyad Symmetry (DS) element in OriP is the essential minimal replicator of OriP. Here, we report the X-ray crystal structure of EBNA1 bound to DS. The structure reveals a previous unrecognized interface formed between dimers of EBNA1 necessary for cooperative DNA-binding, recruitment of cellular replication machinery, and replication function. These findings provide new insights into the mechanism of EBNA1 function at the replication origin and new opportunities to inhibit EBV latent infection and pathogenesis.


    Organizational Affiliation

    Vironika, LLC, Wynnewood, Pennsylvania, USA.,The Wistar Institute, Philadelphia, Pennsylvania, USA.,The Wistar Institute, Philadelphia, Pennsylvania, USA lieberman@wistar.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epstein-Barr nuclear antigen 1
A, B, C, D, I, J, K, L
147Epstein-Barr virus (strain B95-8)Mutation(s): 0 
Gene Names: EBNA1
Find proteins for P03211 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P03211
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (62-MER)E,G62Human herpesvirus 4 strain B95-8
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (62-MER) complementary DNA strandF,H62Human herpesvirus 4 strain B95-8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.118α = 90.00
b = 283.384β = 89.80
c = 63.899γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT096496

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-10-09
    Type: Data collection, Database references