+Open data
-Basic information
Entry | Database: PDB / ID: 3wkj | ||||||
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Title | The nucleosome containing human TSH2B | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / histone variant / histone-fold / DNA binding protein / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information sperm DNA condensation / nucleosome disassembly / mononuclear cell migration / female germ cell nucleus / plasminogen activation / chromosome organization / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus ...sperm DNA condensation / nucleosome disassembly / mononuclear cell migration / female germ cell nucleus / plasminogen activation / chromosome organization / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / epigenetic regulation of gene expression / 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 / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate 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 / Metalloprotease DUBs / 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 / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / UCH proteinases / nucleosome / E3 ubiquitin ligases ubiquitinate target proteins / gene expression / 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 / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / cadherin binding / inflammatory response / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / cell surface / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Urahama, T. / Horikoshi, N. / Osakabe, A. / Tachiwana, H. / Kurumizaka, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Structure of human nucleosome containing the testis-specific histone variant TSH2B. Authors: Urahama, T. / Horikoshi, N. / Osakabe, A. / Tachiwana, H. / Kurumizaka, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wkj.cif.gz | 320.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wkj.ent.gz | 242.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/3wkj ftp://data.pdbj.org/pub/pdb/validation_reports/wk/3wkj | HTTPS FTP |
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-Related structure data
Related structure data | 3afaS 3wkk S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15719.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H3.1 / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68431 #2: Protein | Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H4 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805 #3: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2A / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04908 #4: Protein | Mass: 14480.846 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BA, TSH2B / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96A08 |
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-DNA chain , 1 types, 2 molecules IJ
#5: DNA chain | Mass: 45053.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEM-T Easy / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha |
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-Non-polymers , 3 types, 110 molecules
#6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-MN / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 14, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. all: 54290 / Num. obs: 53677 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 71.115 Å2 / Rsym value: 0.079 / Net I/σ(I): 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AFA Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell |
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