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Yorodumi- PDB-3sow: Structure of UHRF1 PHD finger in complex with histone H3K4me3 1-9... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sow | ||||||
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Title | Structure of UHRF1 PHD finger in complex with histone H3K4me3 1-9 peptide | ||||||
Components |
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Keywords | LIGASE / Zn coordinated PHD finger / Histone binding / Histone H3 | ||||||
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 / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / heterochromatin / telomere organization / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / positive regulation of protein metabolic process / methylated histone binding / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / 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 / Meiotic recombination / replication fork / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / double-strand break repair via homologous recombination / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / RING-type E3 ubiquitin transferase / B-WICH complex positively regulates rRNA expression / euchromatin / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / spindle / structural constituent of chromatin / ubiquitin-protein transferase activity / nucleosome / ubiquitin protein ligase activity / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / histone binding / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nucleic acid binding / protein ubiquitination / cadherin binding / protein heterodimerization activity / 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 / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9501 Å | ||||||
Authors | Rajakumara, E. / Patel, D.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2011 Title: PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression. Authors: Rajakumara, E. / Wang, Z. / Ma, H. / Hu, L. / Chen, H. / Lin, Y. / Guo, R. / Wu, F. / Li, H. / Lan, F. / Shi, Y.G. / Xu, Y. / Patel, D.J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sow.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sow.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 3sow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sow_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 3sow_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 3sow_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3sow_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/3sow ftp://data.pdbj.org/pub/pdb/validation_reports/so/3sow | HTTPS FTP |
-Related structure data
Related structure data | 3souSC 3soxC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | Half of the content in the asymmetric unit that contains protein-peptide complex |
-Components
#1: Protein | Mass: 7920.976 Da / Num. of mol.: 2 / Fragment: UHRF1 (UNP Residues 298-367) Source method: isolated from a genetically manipulated source Details: PreScission protease cleavable N-terminal GST tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ICBP90, NP95, RNF106, UHRF1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | Mass: 1105.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS #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: 2.31 Å3/Da / Density % sol: 46.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: Mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-cooled double Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. obs: 13122 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Rmerge(I) obs: 0.12 / Χ2: 2.338 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3SOU CHAIN A Resolution: 1.9501→19.778 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8331 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.09 / σ(I): 2 / Phase error: 22.41 / 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: 40.842 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.46 Å2 / Biso mean: 29.5322 Å2 / Biso min: 15.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9501→19.778 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: 4
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