[English] 日本語
Yorodumi
- PDB-7vcq: structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vcq
Titlestructure of viral protein BKRF4 in complex with H3.3-H4-ASF1
Components
  • Histone H3.3
  • 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 / viral tegument / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / blastocyst hatching / DNA replication-dependent chromatin assembly / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation ...histone chaperone activity / viral tegument / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / blastocyst hatching / DNA replication-dependent chromatin assembly / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / nucleus organization / spermatid development / single fertilization / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / RNA polymerase II core promoter sequence-specific DNA binding / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / male gonad development / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / spermatogenesis / Estrogen-dependent gene expression / histone binding / cell differentiation / chromosome, telomeric region / cell population proliferation / host cell perinuclear region of cytoplasm / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / host cell nucleus / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 ...Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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 / Orthogonal Bundle / Mainly Alpha
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

#1: Protein Histone H3.3


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more