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- PDB-7wlp: Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to... -

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Basic information

Entry
Database: PDB / ID: 7wlp
TitleEpstein-Barr virus protein BKRF4 restricts nucleosome assembly to suppress host antiviral responses
Components
  • Histone H2B type 1-O,Histone H2A type 1-D
  • Tegument protein BKRF4
KeywordsVIRAL PROTEIN / Epstein-Barr virus / BKRF4 / histones / nucleosomes / DNA double-strand break repair
Function / homology
Function and homology information


viral tegument / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening ...viral tegument / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / UCH proteinases / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Ub-specific processing proteases / host cell perinuclear region of cytoplasm / Amyloid fiber formation / protein heterodimerization activity / host cell nucleus / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 ...Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1-D / Histone H2B type 1-O / Tegument protein BKRF4
Similarity search - Component
Biological speciesHomo sapiens (human)
Human gammaherpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsChen, J. / Shan, S. / Zhou, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970621 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to suppress host antiviral responses.
Authors: Chen, J. / Lu, Z. / Gong, W. / Xiao, X. / Feng, X. / Li, W. / Shan, S. / Xu, D. / Zhou, Z.
History
DepositionJan 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H2B type 1-O,Histone H2A type 1-D
B: Tegument protein BKRF4
D: Tegument protein BKRF4
C: Tegument protein BKRF4


Theoretical massNumber of molelcules
Total (without water)51,1174
Polymers51,1174
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-24 kcal/mol
Surface area10350 Å2
Unit cell
Length a, b, c (Å)88.270, 88.270, 105.626
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Histone H2B type 1-O,Histone H2A type 1-D / H2B-clustered histone 17 / Histone H2B.2 / Histone H2B.n / H2B/n / Histone H2A.3 / Histone H2A/g


Mass: 21364.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Histone H2B and H2A / Source: (gene. exp.) Homo sapiens (human)
Gene: H2BC17, H2BFH, H2BFN, HIST1H2BO, H2AC7, H2AFG, HIST1H2AD
Production host: Escherichia coli (E. coli) / References: UniProt: P23527, UniProt: P20671
#2: Protein Tegument protein BKRF4


Mass: 9917.554 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: GD1 / Gene: BKRF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KSS1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 11406 / % possible obs: 99.7 % / Redundancy: 16.7 % / CC1/2: 1 / Net I/σ(I): 27.7
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1077 / CC1/2: 0.83 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CV5

2cv5


Resolution: 2.29→38.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.583 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.211
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 564 5 %RANDOM
Rwork0.2271 ---
obs0.2278 10817 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.14 Å2 / Biso mean: 62.632 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20.96 Å20 Å2
2--1.92 Å2-0 Å2
3----6.24 Å2
Refinement stepCycle: final / Resolution: 2.29→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 10 1 1516
Biso mean--91.37 78.66 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131527
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151531
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6482055
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5893513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57819.8777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07415280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9321515
X-RAY DIFFRACTIONr_chiral_restr0.080.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021683
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02347
LS refinement shellResolution: 2.295→2.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 28 -
Rwork0.317 757 -
all-785 -
obs--96.67 %

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