7NX5

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 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.282 

wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  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
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
meZRE2 DNA (bottom strand)
C, G
19human gammaherpesvirus 4
Sequence Annotations
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  • Reference Sequence

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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 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.282 
  • 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

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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