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- PDB-7vcq: structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 -

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Basic information

Entry
Database: PDB / ID: 7vcq
Titlestructure of viral protein BKRF4 in complex with H3.3-H4-ASF1
Components
  • Histone H3.3H3F3A
  • Histone H4
  • Histone chaperone ASF1B
  • Tegument protein BKRF4
KeywordsNUCLEAR PROTEIN / H2A-H2B / H3-H4 / histone / Viral protein / nucleosome
Function / homology
Function and homology information


histone chaperone activity / blastocyst hatching / viral tegument / DNA replication-dependent chromatin assembly / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome ...histone chaperone activity / blastocyst hatching / viral tegument / DNA replication-dependent chromatin assembly / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / 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 / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor ...Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Tegument protein BKRF4 / Histone H4 / Histone H3.3 / Histone chaperone ASF1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Epstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLiu, Y.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Epstein-Barr Virus Tegument Protein BKRF4 is a Histone Chaperone.
Authors: Liu, Y. / Li, Y. / Bao, H. / Liu, Y. / Chen, L. / Huang, H.
History
DepositionSep 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
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

Downloads & links

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Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
D: Histone chaperone ASF1B
C: Histone H3.3
E: Histone H4
F: Histone chaperone ASF1B
G: Histone H3.3
H: Histone H4
I: Histone chaperone ASF1B
K: Tegument protein BKRF4


Theoretical massNumber of molelcules
Total (without water)121,92410
Polymers121,92410
Non-polymers00
Water0
1
A: Histone H3.3
B: Histone H4
D: Histone chaperone ASF1B
K: Tegument protein BKRF4


Theoretical massNumber of molelcules
Total (without water)45,7444
Polymers45,7444
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-53 kcal/mol
Surface area16730 Å2
MethodPISA
2
C: Histone H3.3
E: Histone H4
F: Histone chaperone ASF1B


Theoretical massNumber of molelcules
Total (without water)38,0903
Polymers38,0903
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-48 kcal/mol
Surface area15640 Å2
MethodPISA
3
G: Histone H3.3
H: Histone H4
I: Histone chaperone ASF1B


Theoretical massNumber of molelcules
Total (without water)38,0903
Polymers38,0903
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-50 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)286.933, 74.770, 61.191
Angle α, β, γ (deg.)90.000, 97.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histone H3.3 / H3F3A


Mass: 9026.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243
#2: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone chaperone ASF1B / Anti-silencing function protein 1 homolog B / hAsf1 / hAsf1b / CCG1-interacting factor A-II / CIA-II / hCIA-II


Mass: 17668.830 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASF1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVP2
#4: Protein Tegument protein BKRF4


Mass: 7654.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain AG876) / Strain: AG876 / Gene: BKRF4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C724

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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

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 27290 / % possible obs: 98.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 55.61 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134 / Χ2: 0.92 / Net I/σ(I): 4.3 / Num. measured all: 175468
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-3.065.50.65924220.7610.2940.7240.87687.8
3.06-3.185.90.57826290.8330.2510.6320.87195.6
3.18-3.326.10.46227180.9080.20.5040.90898.4
3.32-3.56.20.3327400.9520.1420.360.96399.3
3.5-3.726.80.23127640.9790.0950.2510.963100
3.72-470.18727660.9860.0760.2020.96499.9
4-4.416.70.1228190.9920.050.1311.009100
4.41-5.046.70.08827620.9950.0370.0960.995100
5.04-6.356.80.08527940.9950.0350.0920.878100
6.35-406.40.05128760.9980.0210.0550.74399.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10-2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BNV

5bnv


Resolution: 3→28.31 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 1269 5.39 %
Rwork0.2452 22283 -
obs0.2472 23552 90.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.72 Å2 / Biso mean: 61.4387 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 3→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7402 0 0 0 7402
Num. residues----943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037555
X-RAY DIFFRACTIONf_angle_d0.62510254
X-RAY DIFFRACTIONf_chiral_restr0.0451169
X-RAY DIFFRACTIONf_plane_restr0.0041344
X-RAY DIFFRACTIONf_dihedral_angle_d19.8234566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.120.3581870.288167962
3.12-3.26180.3121200.3002198973
3.2618-3.43350.33081260.2834230885
3.4335-3.64820.31781660.2607259897
3.6482-3.92920.30281540.26292716100
3.9292-4.32330.26751550.23992723100
4.3233-4.9460.28631490.21512754100
4.946-6.22060.28461670.24552741100
6.2206-28.310.22081450.22277599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.96952.16933.60264.76233.44775.9385-0.0720.26670.01280.21350.269-0.2208-0.36210.619-0.18250.42820.00760.13450.2302-0.01910.257767.4841-4.394526.5928
21.4215-0.3124-0.60371.55470.08143.26070.0473-0.11350.1229-0.331-0.0814-0.3355-0.59160.83670.03130.506-0.07570.10910.4286-0.06590.271269.8437-3.792128.1045
32.511-0.53590.35452.14120.12092.2657-0.00520.1634-0.0198-0.0624-0.0082-0.06660.10060.18110.0280.29660.03370.03910.07160.02620.196166.7898-17.39214.7262
42.52350.42660.48453.04530.40731.9375-0.1755-0.1198-0.3067-0.16090.44180.52650.2776-0.6849-0.24030.5305-0.03980.08510.65740.3090.571426.7544-21.03079.989
53.79481.1967-0.5813.19370.14471.5222-0.23860.4501-0.2535-0.31140.63810.5708-0.2298-0.9525-0.33860.5004-0.0320.06120.80440.37040.761424.2074-22.04687.1112
62.5344-0.1181-0.61143.7525-1.21281.9845-0.61350.55890.4622-0.25780.23920.2405-0.2117-0.34060.26150.52-0.088-0.15780.41470.22390.565338.2679-0.7357-0.5619
70.0911-0.1094-0.06510.9589-0.60260.89590.03180.18970.1277-0.30540.57540.51670.1322-0.68270.76170.837-0.3891-0.27211.14540.92821.118817.351718.241942.3619
81.7997-0.878-0.83234.13610.07922.68130.27120.06280.44350.24010.6660.0785-0.1182-0.44751.16020.8396-0.2998-0.44131.12430.83981.108319.613120.565743.2038
92.13411.0096-0.24152.11320.26920.19710.229-0.1126-0.08380.14430.57730.63760.5082-0.851-0.33031.0176-0.4012-0.22351.1890.6651.16028.752434.189322.8667
100.81870.25321.0090.36030.32281.2374-0.0602-0.0762-0.22680.29760.09650.11870.4521-0.53710.12980.7250.02040.25020.7990.04850.409557.8625-10.617740.2041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 60 through 134)A60 - 134
2X-RAY DIFFRACTION2(chain 'B' and resid 17 through 101)B17 - 101
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 155)D1 - 155
4X-RAY DIFFRACTION4(chain 'C' and resid 60 through 133)C60 - 133
5X-RAY DIFFRACTION5(chain 'E' and resid 22 through 101)E22 - 101
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 154)F2 - 154
7X-RAY DIFFRACTION7(chain 'G' and resid 60 through 133)G60 - 133
8X-RAY DIFFRACTION8(chain 'H' and resid 24 through 101)H24 - 101
9X-RAY DIFFRACTION9(chain 'I' and resid 2 through 154)I2 - 154
10X-RAY DIFFRACTION10(chain 'K' and resid 60 through 100)K60 - 100

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