+Open data
-Basic information
Entry | Database: PDB / ID: 8tci | ||||||
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Title | Crystal structure of DNMT3C-DNMT3L in complex with CGG DNA | ||||||
Components |
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Keywords | TRANSFERASE / DNA cytosine methyltransferase | ||||||
Function / homology | Function and homology information : / piRNA-mediated retrotransposon silencing by heterochromatin formation / retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / genomic imprinting / homologous chromosome pairing at meiosis / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity ...: / piRNA-mediated retrotransposon silencing by heterochromatin formation / retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / genomic imprinting / homologous chromosome pairing at meiosis / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / negative regulation of DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / DNA methylation-dependent heterochromatin formation / negative regulation of gene expression, epigenetic / male meiosis I / catalytic complex / heterochromatin / enzyme activator activity / DNA methylation / condensed nuclear chromosome / stem cell differentiation / placenta development / spermatogenesis / methylation / cell differentiation / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å | ||||||
Authors | Khudaverdyan, N. / Song, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: The structure of DNA methyltransferase DNMT3C reveals an activity-tuning mechanism for DNA methylation. Authors: Khudaverdyan, N. / Lu, J. / Chen, X. / Herle, G. / Song, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tci.cif.gz | 442.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tci.ent.gz | 356.3 KB | Display | PDB format |
PDBx/mmJSON format | 8tci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/8tci ftp://data.pdbj.org/pub/pdb/validation_reports/tc/8tci | HTTPS FTP |
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-Related structure data
Related structure data | 6u8pS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32535.496 Da / Num. of mol.: 2 / Fragment: UNP residues 458-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt3c, Gm14490 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DOY1, DNA (cytosine-5-)-methyltransferase #2: Protein | Mass: 23024.424 Da / Num. of mol.: 2 / Fragment: UNP residues 181-379 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UJW3 #3: DNA chain | Mass: 7370.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) #4: Chemical | Has ligand of interest | N | |
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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: 2.98 Å3/Da / Density % sol: 58.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 2% v/v Tacsimate, pH 8.0, 0.1 M Tris, pH 8.5, 16% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.19→50 Å / Num. obs: 23776 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.93 / CC star: 0.982 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.118 / Rrim(I) all: 0.224 / Χ2: 5.874 / Net I/σ(I): 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6U8P Resolution: 3.19→44.56 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.19→44.56 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.3682 Å / Origin y: -2.9605 Å / Origin z: 15.6081 Å
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Refinement TLS group | Selection details: all |