5T7X

Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency.

Dheekollu, J.Malecka, K.Wiedmer, A.Delecluse, H.J.Chiang, A.K.Altieri, D.C.Messick, T.E.Lieberman, P.M.

(2017) Oncotarget 8: 7248-7264

  • DOI: 10.18632/oncotarget.14540
  • Primary Citation of Related Structures:  
    5T7X

  • PubMed Abstract: 
  • Epstein-Barr Virus (EBV) latent infection is a causative co-factor for endemic Nasopharyngeal Carcinoma (NPC). NPC-associated variants have been identified in EBV-encoded nuclear antigen EBNA1. Here, we solve the X-ray crystal structure of an NPC-derived EBNA1 DNA binding domain (DBD) and show that variant amino acids are found on the surface away from the DNA binding interface ...

    Epstein-Barr Virus (EBV) latent infection is a causative co-factor for endemic Nasopharyngeal Carcinoma (NPC). NPC-associated variants have been identified in EBV-encoded nuclear antigen EBNA1. Here, we solve the X-ray crystal structure of an NPC-derived EBNA1 DNA binding domain (DBD) and show that variant amino acids are found on the surface away from the DNA binding interface. We show that NPC-derived EBNA1 is compromised for DNA replication and episome maintenance functions. Recombinant virus containing the NPC EBNA1 DBD are impaired in their ability to immortalize primary B-lymphocytes and suppress lytic transcription during early stages of B-cell infection. We identify Survivin as a host protein deficiently bound by the NPC variant of EBNA1 and show that Survivin depletion compromises EBV episome maintenance in multiple cell types. We propose that endemic variants of EBNA1 play a significant role in EBV-driven carcinogenesis by altering key regulatory interactions that destabilize latent infection.


    Organizational Affiliation

    The Wistar Institute, Philadelphia, PA USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Epstein-Barr nuclear antigen 1C [auth A], D [auth B]149Human herpesvirus 4 strain B95-8Mutation(s): 1 
Gene Names: EBNA1BKRF1
UniProt
Find proteins for Q3KSS4 (Epstein-Barr virus (strain GD1))
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Go to UniProtKB:  Q3KSS4
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3')A [auth C]18Human herpesvirus 4 strain B95-8
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3')B [auth D]18Human herpesvirus 4 strain B95-8
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.35 Å
      • R-Value Free: 0.233 
      • R-Value Work: 0.185 
      • R-Value Observed: 0.190 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 60.025α = 90
      b = 64.904β = 90
      c = 111.783γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-3000data reduction
      HKL-3000data scaling
      HKL-3000phasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2017-07-19
        Type: Initial release