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Yorodumi- PDB-4gy5: Crystal structure of the tandem tudor domain and plant homeodomai... -
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-Basic information
Entry | Database: PDB / ID: 4gy5 | ||||||
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Title | Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 | ||||||
Components |
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Keywords | LIGASE / Histone binding | ||||||
Function / homology | Function and homology information histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / negative regulation of chromosome condensation / hemi-methylated DNA-binding / Barr body / regulation of centromere complex assembly / homologous recombination / muscle cell differentiation ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / negative regulation of chromosome condensation / hemi-methylated DNA-binding / Barr body / regulation of centromere complex assembly / homologous recombination / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / regulation of epithelial cell proliferation / methyl-CpG binding / oocyte maturation / negative regulation of gene expression via chromosomal CpG island methylation / nucleus organization / spermatid development / mitotic spindle assembly / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin formation / epigenetic regulation of gene expression / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / methylated histone binding / telomere organization / positive regulation of protein metabolic process / RNA Polymerase I Promoter Opening / embryo implantation / 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) / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RING-type E3 ubiquitin transferase / 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 / multicellular organism growth / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / Transcriptional regulation of granulopoiesis / osteoblast differentiation / structural constituent of chromatin / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / histone binding / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / nucleic acid binding / chromosome, telomeric region / protein ubiquitination / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.956 Å | ||||||
Authors | Cheng, J. / Yang, Y. / Fang, J. / Xiao, J. / Zhu, T. / Chen, F. / Wang, P. / Xu, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing ...Title: Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein Authors: Cheng, J. / Yang, Y. / Fang, J. / Xiao, J. / Zhu, T. / Chen, F. / Wang, P. / Li, Z. / Yang, H. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gy5.cif.gz | 168.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gy5.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 4gy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gy5_validation.pdf.gz | 487.4 KB | Display | wwPDB validaton report |
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Full document | 4gy5_full_validation.pdf.gz | 509.8 KB | Display | |
Data in XML | 4gy5_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 4gy5_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/4gy5 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/4gy5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 27794.279 Da / Num. of mol.: 4 / Fragment: Tudor PHD domain, UNP residues 134-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1 / Production host: Escherichia coli (E. coli) References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | Mass: 1862.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243 #3: Chemical | ChemComp-ZN / #4: 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: 2.92 Å3/Da / Density % sol: 57.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97927 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2012 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2.956→50 Å / Num. all: 27861 / Num. obs: 27861 / % possible obs: 100 % / Biso Wilson estimate: 82.9 Å2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DB3, 3SHB Resolution: 2.956→45.377 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7655 / SU ML: 0.39 / σ(F): 0.16 / Phase error: 29.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.719 Å2 / ksol: 0.279 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 229.78 Å2 / Biso mean: 97.4127 Å2 / Biso min: 33.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.956→45.377 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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