7VCQ

structure of viral protein BKRF4 in complex with H3.3-H4-ASF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Epstein-Barr Virus Tegument Protein BKRF4 is a Histone Chaperone.

Liu, Y.Li, Y.Bao, H.Liu, Y.Chen, L.Huang, H.

(2022) J Mol Biol 434: 167756-167756

  • DOI: https://doi.org/10.1016/j.jmb.2022.167756
  • Primary Citation of Related Structures:  
    7VCL, 7VCQ

  • PubMed Abstract: 

    Histone chaperones, which constitute an interaction and functional network involved in all aspects of histone metabolism, have to date been identified only in eukaryotes. The Epstein-Barr virus tegument protein BKRF4 is a histone-binding protein that engages histones H2A-H2B and H3-H4, and cellular chromatin, inhibiting the host DNA damage response. Here, we identified BKRF4 as a bona fide viral histone chaperone whose histone-binding domain (HBD) forms a co-chaperone complex with the human histone chaperone ASF1 in vitro. We determined the crystal structures of the quaternary complex of the BKRF4 HBD with human H3-H4 dimer and the histone chaperone ASF1b and the ternary complex of the BKRF4 HBD with human H2A-H2B dimer. Through structural and biochemical studies, we elucidated the molecular basis for H3-H4 and H2A-H2B recognition by BKRF4. We also revealed two conserved motifs, D/EL and DEF/Y/W, within the BKRF4 HBD, which may represent common motifs through which histone chaperones target H3-H4 and H2A-H2B, respectively. In conclusion, our results identify BKRF4 as a histone chaperone encoded by the Epstein-Barr virus, representing a typical histone chaperone found in a non-eukaryote. We envision that more histone chaperones await identification and characterization in DNA viruses and even archaea.


  • Organizational Affiliation

    Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: yongrui@mail.ustc.edu.cn.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3A,
D [auth C],
G
79Homo sapiensMutation(s): 0 
Gene Names: H3-3AH3.3AH3F3H3F3APP781H3-3BH3.3BH3F3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
PHAROS:  P84243
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UniProt GroupP84243
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, E, H
103Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
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PHAROS:  P62805
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UniProt GroupP62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone chaperone ASF1BC [auth D],
F,
I
156Homo sapiensMutation(s): 0 
Gene Names: ASF1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVP2 (Homo sapiens)
Explore Q9NVP2 
Go to UniProtKB:  Q9NVP2
PHAROS:  Q9NVP2
GTEx:  ENSG00000105011 
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UniProt GroupQ9NVP2
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tegument protein BKRF4J [auth K]70Epstein-barr virus strain ag876Mutation(s): 0 
Gene Names: BKRF4
UniProt
Find proteins for P30117 (Epstein-Barr virus (strain B95-8))
Explore P30117 
Go to UniProtKB:  P30117
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UniProt GroupP30117
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 286.933α = 90
b = 74.77β = 97.5
c = 61.191γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-08-03 
  • Deposition Author(s): Liu, Y.R.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description