+Open data
-Basic information
Entry | Database: PDB / ID: 6kdt | ||||||
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Title | Crystal structure of human DNMT3B (Q772R)-DNMT3L complex | ||||||
Components |
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Keywords | TRANSFERASE / DNMT3B / DNA methyltransferase / complex | ||||||
Function / homology | Function and homology information retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / negative regulation of DNA methylation-dependent 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 / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / negative regulation of DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / DNA metabolic process / negative regulation of gene expression, epigenetic / male meiosis I / catalytic complex / heterochromatin / enzyme activator activity / DNA methylation / PRC2 methylates histones and DNA / condensed nuclear chromosome / Defective pyroptosis / stem cell differentiation / NoRC negatively regulates rRNA expression / placenta development / transcription corepressor activity / methylation / spermatogenesis / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å | ||||||
Authors | Lin, C.-C. / Chen, Y.-P. / Yang, W.-Z. / Shen, C.-K. / Yuan, H.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B. Authors: Lin, C.C. / Chen, Y.P. / Yang, W.Z. / Shen, J.C.K. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kdt.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kdt.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kdt_validation.pdf.gz | 990.9 KB | Display | wwPDB validaton report |
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Full document | 6kdt_full_validation.pdf.gz | 1004.7 KB | Display | |
Data in XML | 6kdt_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 6kdt_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kdt ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kdt | HTTPS FTP |
-Related structure data
Related structure data | 6kdaC 6kdbC 6kdlC 6kdpC 5yx2S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32744.926 Da / Num. of mol.: 2 / Mutation: Q772R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli) References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase #2: Protein | Mass: 23627.107 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJW3 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.74 Å3/Da / Density % sol: 67.11 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / Details: 2.2 M sodium formate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30 Å / Num. obs: 36776 / % possible obs: 97.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 13.24 |
Reflection shell | Resolution: 2.85→2.95 Å / Num. unique obs: 2796 / CC1/2: 0.824 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YX2 Resolution: 2.87→27.37 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.87→27.37 Å
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LS refinement shell | Resolution: 2.867→2.94 Å
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