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- PDB-3f8i: Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal st... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f8i | ||||||
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Title | Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21 | ||||||
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![]() | LIGASE/DNA / UHRF1 / 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 / Ubl conjugation pathway / Zinc / Zinc-finger / LIGASE-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hashimoto, H. / Horton, J.R. / Zhang, X. / Cheng, X. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.2 KB | Display | ![]() |
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PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3f8jC ![]() 3fdeC ![]() 2zo0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | Asymmetric unit contains two SRA-DNA complexes. |
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Components
#1: Protein | Mass: 23915.711 Da / Num. of mol.: 2 / Fragment: YDG domain: UNP residues 419-628 Source method: isolated from a genetically manipulated source Details: hexahistidine-SUMO-tagged construct / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 3637.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA oligo #3: DNA chain | Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA oligo #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.15 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 7 Details: 20% PEG 3350, 0.4M 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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→34.53 Å / Num. obs: 30041 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.3 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZO0 Resolution: 2.29→34.53 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 622448.07 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.0138 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.29→34.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.37 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
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Xplor file |
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