7WLP

Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to suppress host antiviral responses


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to suppress host antiviral responses.

Chen, J.Lu, Z.Gong, W.Xiao, X.Feng, X.Li, W.Shan, S.Xu, D.Zhou, Z.

(2022) Proc Natl Acad Sci U S A 119: e2203782119-e2203782119

  • DOI: https://doi.org/10.1073/pnas.2203782119
  • Primary Citation of Related Structures:  
    7WLP

  • PubMed Abstract: 

    Inhibition of host DNA damage response (DDR) is a common mechanism used by viruses to manipulate host cellular machinery and orchestrate viral life cycles. Epstein-Barr virus tegument protein BKRF4 associates with cellular chromatin to suppress host DDR signaling, but the underlying mechanism remains elusive. Here, we identify a BKRF4 histone binding domain (residues 15-102, termed BKRF4-HBD) that can accumulate at the DNA damage sites to disrupt 53BP1 foci formation. The high-resolution structure of the BKRF4-HBD in complex with a human H2A-H2B dimer shows that BKRF4-HBD interacts with the H2A-H2B dimer via the N-terminal region (NTR), the DWP motif (residues 80-86 containing D81, W84, P86), and the C-terminal region (CTR). The "triple-anchor" binding mode confers BKRF4-HBD the ability to associate with the partially unfolded nucleosomes, promoting the nucleosome disassembly. Importantly, disrupting the BKRF4-H2A-H2B interaction impairs the binding between BKRF4-HBD and nucleosome in vitro and inhibits the recruitment of BKRF4-HBD to DNA breaks in vivo. Together, our study reveals the structural basis of BKRF4 bindings to the partially unfolded nucleosome and elucidates an unconventional mechanism of host DDR signal attenuation.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-O,Histone H2A type 1-D193Homo sapiensMutation(s): 0 
Gene Names: H2BC17H2BFHH2BFNHIST1H2BOH2AC7H2AFGHIST1H2AD
UniProt & NIH Common Fund Data Resources
Find proteins for P23527 (Homo sapiens)
Explore P23527 
Go to UniProtKB:  P23527
PHAROS:  P23527
GTEx:  ENSG00000274641 
Find proteins for P20671 (Homo sapiens)
Explore P20671 
Go to UniProtKB:  P20671
PHAROS:  P20671
GTEx:  ENSG00000196866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP23527P20671
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tegument protein BKRF4B,
C [auth D],
D [auth C]
88human gammaherpesvirus 4Mutation(s): 0 
Gene Names: BKRF4
UniProt
Find proteins for Q3KSS1 (Epstein-Barr virus (strain GD1))
Explore Q3KSS1 
Go to UniProtKB:  Q3KSS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3KSS1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.27α = 90
b = 88.27β = 90
c = 105.626γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31970621

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description