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- PDB-7wlp: Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wlp | ||||||
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Title | Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to suppress host antiviral responses | ||||||
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![]() | VIRAL PROTEIN / Epstein-Barr virus / BKRF4 / histones / nucleosomes / DNA double-strand break repair | ||||||
Function / homology | ![]() viral tegument / heterochromatin organization / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere ...viral tegument / heterochromatin organization / 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 / nucleosomal DNA binding / 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 / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / 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 / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Ub-specific processing proteases / protein heterodimerization activity / Amyloid fiber formation / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, J. / Shan, S. / Zhou, Z. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.4 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.7 KB | Display | ![]() |
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Full document | ![]() | 451.9 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cv5S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | 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.) ![]() Gene: H2BC17, H2BFH, H2BFN, HIST1H2BO, H2AC7, H2AFG, HIST1H2AD Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 9917.554 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: GD1 / Gene: BKRF4 / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium sulfate |
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-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. obs: 11406 / % possible obs: 99.7 % / Redundancy: 16.7 % / CC1/2: 1 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.14 Å2 / Biso mean: 62.632 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.29→38.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.295→2.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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