5KDM

Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis underlying viral hijacking of a histone chaperone complex.

Huang, H., Deng, Z., Vladimirova, O., Wiedmer, A., Lu, F., Lieberman, P.M., Patel, D.J.

(2016) Nat Commun 7: 12707-12707

  • DOI: 10.1038/ncomms12707
  • Primary Citation of Related Structures:  
    5KDM

  • PubMed Abstract: 

    • The histone H3.3 chaperone DAXX is implicated in formation of heterochromatin and transcription silencing, especially for newly infecting DNA virus genomes entering the nucleus. Epstein-Barr virus (EBV) can efficiently establish stable latent infection as a chromatinized episome in the nucleus of infected cells ...

    The histone H3.3 chaperone DAXX is implicated in formation of heterochromatin and transcription silencing, especially for newly infecting DNA virus genomes entering the nucleus. Epstein-Barr virus (EBV) can efficiently establish stable latent infection as a chromatinized episome in the nucleus of infected cells. The EBV tegument BNRF1 is a DAXX-interacting protein required for the establishment of selective viral gene expression during latency. Here we report the structure of BNRF1 DAXX-interaction domain (DID) in complex with DAXX histone-binding domain (HBD) and histones H3.3-H4. BNRF1 DID contacts DAXX HBD and histones through non-conserved loops. The BNRF1-DAXX interface is responsible for BNRF1 localization to PML-nuclear bodies typically associated with host-antiviral resistance and transcriptional repression. Paradoxically, the interface is also required for selective transcription activation of viral latent cycle genes required for driving B-cell proliferation. These findings reveal molecular details of virus reprogramming of an antiviral histone chaperone to promote viral latency and cellular immortalization.

    Organizational Affiliation: 

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3A135Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B, H3-3A, H3-3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
PHAROS:  P84243
GTEx:  ENSG00000163041 
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UniProt GroupP84243
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B102Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Death domain-associated protein 6C212Homo sapiensMutation(s): 0 
Gene Names: DAXX, BING2, DAP6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UER7 (Homo sapiens)
Explore Q9UER7 
Go to UniProtKB:  Q9UER7
PHAROS:  Q9UER7
GTEx:  ENSG00000204209 
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UniProt GroupQ9UER7
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Major tegument proteinD219Epstein-barr virus strain ag876Mutation(s): 0 
Gene Names: BNRF1
UniProt
Find proteins for Q1HVJ0 (Epstein-Barr virus (strain AG876))
Explore Q1HVJ0 
Go to UniProtKB:  Q1HVJ0
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UniProt GroupQ1HVJ0
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.216α = 90
b = 161.216β = 90
c = 117.772γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2016-06-08 
  • Released Date: 2016-09-07 
    • Deposition Author(s): Huang, H., Patel, D.

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy