2C9L

Structure of the Epstein-Barr virus ZEBRA protein

• PDB DOI: https://doi.org/10.2210/pdb2C9L/pdb
• NAKB: 2C9L

• Classification: VIRAL PROTEIN
• Organism(s): human gammaherpesvirus 4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-12-13 Released: 2006-02-21 
• Deposition Author(s): Petosa, C., Morand, P., Baudin, F., Moulin, M., Artero, J.B., Muller, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.264 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 

Literature

Structural Basis of Lytic Cycle Activation by the Epstein-Barr Virus Zebra Protein

Petosa, C., Morand, P., Baudin, F., Moulin, M., Artero, J.B., Muller, C.W.

(2006) Mol Cell 21: 565

• PubMed: 16483937 
• DOI: https://doi.org/10.1016/j.molcel.2006.01.006
• Primary Citation of Related Structures:  
  2C9L, 2C9N


• PubMed Abstract: 
  

  Epstein-Barr virus (EBV) causes infectious mononucleosis and is linked to several human malignancies. EBV has a biphasic infection cycle consisting of a latent and a lytic, replicative phase. The switch from latent to lytic infection is triggered by the EBV immediate-early transcription factor ZEBRA (BZLF1, Zta, Z, EB1). We present the crystal structure of ZEBRA's DNA binding domain bound to an EBV lytic gene promoter element. ZEBRA exhibits a variant of the basic-region leucine zipper (bZIP) fold in which a C-terminal moiety stabilizes the coiled coil involved in dimer formation. The structure provides insights into ZEBRA's broad target site specificity, preferential activation of specific EBV promoters in their methylated state, ability to dimerize despite lacking a leucine zipper motif, and failure to heterodimerize with cellular bZIP proteins. The structure will allow for the design of new therapeutic agents that block activation of the EBV lytic cycle.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Grenoble Outstation, B.P. 181, 38042 Grenoble Cedex 9, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 26.17 kDa 
• Atom Count: 1,878 
• Modelled Residue Count: 162 
• Deposited Residue Count: 163 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BZLF1 TRANS-ACTIVATOR PROTEIN	C [auth Y], D [auth Z]	63	human gammaherpesvirus 4	Mutation(s): 2
UniProt
Find proteins for P03206 (Epstein-Barr virus (strain B95-8)) Explore P03206  Go to UniProtKB:  P03206

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*CP *TP*CP*AP*TP*GP*AP*AP*GP*T)-3'	A	19	human gammaherpesvirus 4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*TP*TP*CP*AP*CP*TP*GP*AP *GP*TP*CP*AP*GP*TP*GP*CP*T)-3'	B	18	human gammaherpesvirus 4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.264 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.17	α = 90
b = 26.52	β = 103.95
c = 98.09	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-21 
Deposition Author(s): Petosa, C., Morand, P., Baudin, F., Moulin, M., Artero, J.B., Muller, C.W.

Revision History  

• Version 1.0: 2006-02-21
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description