7NX5 | pdb_00007nx5

Crystal structure of the Epstein-Barr Virus protein ZEBRA (BZLF1, Zta) bound to a methylated DNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.339 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.277 (Depositor) 
  • R-Value Observed: 
    0.282 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7NX5

This is version 1.2 of the entry. See complete history

Literature

Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1.

Bernaudat, F.Gustems, M.Gunther, J.Oliva, M.F.Buschle, A.Gobel, C.Pagniez, P.Lupo, J.Signor, L.Muller, C.W.Morand, P.Sattler, M.Hammerschmidt, W.Petosa, C.

(2022) Nucleic Acids Res 50: 490-511

  • DOI: https://doi.org/10.1093/nar/gkab1183
  • Primary Citation Related Structures: 
    7NX5

  • PubMed Abstract: 

    In infected cells, Epstein-Barr virus (EBV) alternates between latency and lytic replication. The viral bZIP transcription factor ZEBRA (Zta, BZLF1) regulates this cycle by binding to two classes of ZEBRA response elements (ZREs): CpG-free motifs resembling the consensus AP-1 site recognized by cellular bZIP proteins and CpG-containing motifs that are selectively bound by ZEBRA upon cytosine methylation. We report structural and mutational analysis of ZEBRA bound to a CpG-methylated ZRE (meZRE) from a viral lytic promoter. ZEBRA recognizes the CpG methylation marks through a ZEBRA-specific serine and a methylcytosine-arginine-guanine triad resembling that found in canonical methyl-CpG binding proteins. ZEBRA preferentially binds the meZRE over the AP-1 site but mutating the ZEBRA-specific serine to alanine inverts this selectivity and abrogates viral replication. Our findings elucidate a DNA methylation-dependent switch in ZEBRA's transactivation function that enables ZEBRA to bind AP-1 sites and promote viral latency early during infection and subsequently, under appropriate conditions, to trigger EBV lytic replication by binding meZREs.


  • Organizational Affiliation
    • Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 53.07 kDa 
  • Atom Count: 3,158 
  • Modeled Residue Count: 303 
  • Deposited Residue Count: 328 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Trans-activator protein BZLF1
A, B, E, F
63Human herpesvirus 4 strain B95-8Mutation(s): 1 
Gene Names: BZLF1
UniProt
Find proteins for P03206 (Epstein-Barr virus (strain B95-8))
Explore P03206 
Go to UniProtKB:  P03206
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03206
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
meZRE2 DNA (bottom strand)
C, G
19human gammaherpesvirus 4
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
meZRE2 DNA (top strand)
D, H
19human gammaherpesvirus 4
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.339 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.277 (Depositor) 
  • R-Value Observed: 0.282 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.99α = 90
b = 26.56β = 103.104
c = 80.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-INBS-05-02
Agence Nationale de la Recherche (ANR)FranceANR-17-EURE-0003

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description