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
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS  P84243
GTEx  ENSG00000163041
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B102Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Death domain-associated protein 6C212Homo sapiensMutation(s): 0 
Gene Names: DAXX, BING2, DAP6
Find proteins for Q9UER7 (Homo sapiens)
Explore Q9UER7 
Go to UniProtKB:  Q9UER7
NIH Common Fund Data Resources
PHAROS  Q9UER7
GTEx  ENSG00000204209
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Major tegument proteinD219Epstein-barr virus strain ag876Mutation(s): 0 
Gene Names: BNRF1
Find proteins for Q1HVJ0 (Epstein-Barr virus (strain AG876))
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Go to UniProtKB:  Q1HVJ0
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  • Reference Sequence
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 

  • 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