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Yorodumi- PDB-3swc: GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3swc | ||||||
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Title | GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide | ||||||
Components |
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Keywords | TRANSFERASE / epigenetics / non-histone lysine methylation / SET domain / protein lysine methyltransferase | ||||||
Function / homology | Function and homology information DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / : / : / : / epigenetic programming of gene expression / positive regulation of cellular response to hypoxia / PRC2 methylates histones and DNA / [histone H3]-lysine9 N-methyltransferase / cellular response to bisphenol A / peptidyl-lysine monomethylation ...DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / : / : / : / epigenetic programming of gene expression / positive regulation of cellular response to hypoxia / PRC2 methylates histones and DNA / [histone H3]-lysine9 N-methyltransferase / cellular response to bisphenol A / peptidyl-lysine monomethylation / protein-cysteine methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / RMTs methylate histone arginines / genomic imprinting / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / protein-lysine N-methyltransferase activity / XY body / C2H2 zinc finger domain binding / response to vitamin A / cellular response to ethanol / DNA methylation-dependent heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / Transcriptional Regulation by E2F6 / regulation of embryonic development / chromosome, centromeric region / catalytic complex / Transcriptional Regulation by VENTX / heterochromatin / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to amino acid stimulus / transcription corepressor binding / response to cocaine / methyltransferase activity / response to lead ion / PKMTs methylate histone lysines / euchromatin / Regulation of TP53 Activity through Methylation / neuron differentiation / p53 binding / response to toxic substance / nuclear matrix / chromatin organization / response to estradiol / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / positive regulation of cold-induced thermogenesis / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.332 Å | ||||||
Authors | Chang, Y. / Horton, J.R. / Zhang, X. / Cheng, X. | ||||||
Citation | Journal: Nat Commun / Year: 2011 Title: MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Authors: Chang, Y. / Sun, L. / Kokura, K. / Horton, J.R. / Fukuda, M. / Espejo, A. / Izumi, V. / Koomen, J.M. / Bedford, M.T. / Zhang, X. / Shinkai, Y. / Fang, J. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3swc.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3swc.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 3swc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3swc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3swc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3swc_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 3swc_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/3swc ftp://data.pdbj.org/pub/pdb/validation_reports/sw/3swc | HTTPS FTP |
-Related structure data
Related structure data | 3svmC 3sw9C 3mo5S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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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Unit cell |
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-Components
#1: Protein | Mass: 32830.219 Da / Num. of mol.: 2 / Fragment: unp residues 982-1266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D / Plasmid: pXC681 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H9B1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1286.509 Da / Num. of mol.: 2 / Fragment: unp residues 39-50 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) References: UniProt: O88508, DNA (cytosine-5-)-methyltransferase #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→40.78 Å / Num. obs: 29318 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.33→2.4 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 5.6 / Num. unique all: 2825 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 3MO5 Resolution: 2.332→40.78 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 22.5 / 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: 31.413 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.332→40.78 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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