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Yorodumi- PDB-5yy9: Crystal structure of Tandem Tudor Domain of human UHRF1 in comple... -
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-Basic information
Entry | Database: PDB / ID: 5yy9 | ||||||
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Title | Crystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3 | ||||||
Components |
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Keywords | TRANSFERASE / Maintenance of DNA methylation | ||||||
Function / homology | Function and homology information Okazaki fragment processing involved in mitotic DNA replication / histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA ligase activity / DNA damage sensor activity / DNA ligase (ATP) / DNA ligase (ATP) activity / hemi-methylated DNA-binding / homologous recombination ...Okazaki fragment processing involved in mitotic DNA replication / histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA ligase activity / DNA damage sensor activity / DNA ligase (ATP) / DNA ligase (ATP) activity / hemi-methylated DNA-binding / homologous recombination / Processive synthesis on the lagging strand / DNA ligation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / regulation of epithelial cell proliferation / lagging strand elongation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / DNA biosynthetic process / Early Phase of HIV Life Cycle / mitotic spindle assembly / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / mismatch repair / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / base-excision repair / nuclear matrix / spindle / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / DNA recombination / nucleic acid binding / protein ubiquitination / cell division / intracellular membrane-bounded organelle / DNA repair / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 Å | ||||||
Authors | Kori, S. / Defossez, P.A. / Arita, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Structure / Year: 2019 Title: Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation. Authors: Kori, S. / Ferry, L. / Matano, S. / Jimenji, T. / Kodera, N. / Tsusaka, T. / Matsumura, R. / Oda, T. / Sato, M. / Dohmae, N. / Ando, T. / Shinkai, Y. / Defossez, P.A. / Arita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yy9.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yy9.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 5yy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yy9_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 5yy9_full_validation.pdf.gz | 456 KB | Display | |
Data in XML | 5yy9_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5yy9_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/5yy9 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/5yy9 | HTTPS FTP |
-Related structure data
Related structure data | 5yyaC 3db3S 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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Unit cell |
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-Components
#1: Protein | Mass: 18162.207 Da / Num. of mol.: 2 / Fragment: Tandem Tudor Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: Q96T88, RING-type E3 ubiquitin transferase #2: Protein/peptide | Mass: 1640.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P18858*PLUS #3: 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: 2.1 Å3/Da / Density % sol: 41.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 00 mM Tris-HCl (pH 7.0), 200 mM tri-potassium phosphate and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→48.67 Å / Num. obs: 40019 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.95 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DB3 Resolution: 2.653→40.228 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.653→40.228 Å
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Refine LS restraints |
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LS refinement shell |
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