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Yorodumi- PDB-3f8j: Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f8j | ||||||
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Title | Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group C222(1) | ||||||
Components |
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Keywords | LIGASE/DNA / UHRF1 / SRA / base flipping / 5-methylcytosine / CpG methylation / Cell cycle / Developmental protein / DNA damage / DNA repair / DNA-binding / Ligase / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation pathway / Zinc-finger / LIGASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / 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 / positive regulation of protein metabolic process ...histone H3 ubiquitin ligase activity / hemi-methylated DNA-binding / 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 / positive regulation of protein metabolic process / methylated histone binding / replication fork / RING-type E3 ubiquitin transferase / euchromatin / heterochromatin formation / nuclear matrix / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Hashimoto, H. / Horton, J.R. / Zhang, X. / Cheng, X. | ||||||
Citation | Journal: Epigenetics / Year: 2009 Title: UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Authors: Hashimoto, H. / Horton, J.R. / Zhang, X. / Cheng, X. #1: Journal: Nature / Year: 2008 Title: The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Authors: Hashimoto, H. / Horton, J.R. / Zhang, X. / Bostick, M. / Jacobsen, S.E. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f8j.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f8j.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 3f8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/3f8j ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f8j | HTTPS FTP |
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-Related structure data
Related structure data | 3f8iC 3fdeC 2zo0S 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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1 |
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Unit cell |
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Details | One SRA-DNA complex per asymmetric unit |
-Components
#1: Protein | Mass: 23858.656 Da / Num. of mol.: 1 / Fragment: YDG domain: UNP residues 417-628 Source method: isolated from a genetically manipulated source Details: hexahistidine-SUMO-tagged construct / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uhrf1 / Plasmid: pXC675 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDF2 | ||||
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#2: DNA chain | Mass: 3637.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA oligo | ||||
#3: DNA chain | Mass: 3703.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA oligo | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | AUTHORS USED NATIVE SEQUENCE ILE VAL FOR RESIDUES 417 AND 418 IN THIS ENTRY (WITHOUT ANY EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 7 Details: 20% PEG 3350, 0.4 M NaCl, pH 7.0, VAPOR DIFFUSION, temperature 277K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→29.91 Å / Num. obs: 23488 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.6 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZO0 Resolution: 1.99→29.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 412547.2 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Bsol: 46.64 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.99→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.06 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
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Xplor file |
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