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- PDB-6f57: Crystal structure of DNMT3A-DNMT3L in complex with single CpG-con... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f57 | |||||||||
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Title | Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA | |||||||||
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![]() | transferase/DNA / DNMT3A / DNMT3L / DNA methylation / DNA binding protein / transferase-DNA complex | |||||||||
Function / homology | ![]() retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase ...retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / negative regulation of DNA methylation-dependent heterochromatin formation / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / XY body / cellular response to ethanol / response to vitamin A / negative regulation of gene expression via chromosomal CpG island methylation / DNA metabolic process / negative regulation of gene expression, epigenetic / response to ionizing radiation / hepatocyte apoptotic process / male meiosis I / chromosome, centromeric region / catalytic complex / heterochromatin / enzyme activator activity / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / PRC2 methylates histones and DNA / response to cocaine / condensed nuclear chromosome / Defective pyroptosis / stem cell differentiation / cellular response to amino acid stimulus / response to lead ion / euchromatin / placenta development / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / transcription corepressor activity / response to estradiol / cellular response to hypoxia / methylation / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
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Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, Z.M. / Song, J. | |||||||||
![]() | ![]() Title: Structural basis for DNMT3A-mediated de novo DNA methylation. Authors: Zhang, Z.M. / Lu, R. / Wang, P. / Yu, Y. / Chen, D. / Gao, L. / Liu, S. / Ji, D. / Rothbart, S.B. / Wang, Y. / Wang, G.G. / Song, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 395.6 KB | Display | ![]() |
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PDB format | ![]() | 318.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1003.9 KB | Display | ![]() |
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Full document | ![]() | 1016.6 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yx2C ![]() 6brrC ![]() 2qrvS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32715.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase #2: Protein | Mass: 24163.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: DNA chain | Mass: 3094.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: DNA chain | Mass: 3270.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.12 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 7% PEG4000, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2, 166 mM imidazole (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→47.72 Å / Num. obs: 26661 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3.09→3.2 Å / Rmerge(I) obs: 0.982 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QRV Resolution: 3.098→47.72 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.67 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.098→47.72 Å
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Refine LS restraints |
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LS refinement shell |
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