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Open data
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Basic information
Entry | Database: PDB / ID: 4u7p | ||||||
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Title | Crystal structure of DNMT3A-DNMT3L complex | ||||||
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![]() | TRANSFERASE/TRANSFERASE REGULATOR / DNA methyltransferase / autoinhibitory form / TRANSFERASE-TRANSFERASE REGULATOR 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wang, L. / Guo, X. / Li, J. / Xiao, J. / Yin, X. / He, S. / Wang, J. / Xu, Y. | ||||||
![]() | ![]() Title: Structural insight into autoinhibition and histone H3-induced activation of DNMT3A Authors: Guo, X. / Wang, L. / Li, J. / Ding, Z. / Xiao, J. / Yin, X. / He, S. / Shi, P. / Dong, L. / Li, G. / Tian, C. / Wang, J. / Cong, Y. / Xu, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.8 KB | Display | ![]() |
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PDB format | ![]() | 109.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 696.8 KB | Display | ![]() |
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Full document | ![]() | 714.9 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u7tC ![]() 2qrvS ![]() 3a1aS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 53350.352 Da / Num. of mol.: 1 / Fragment: UNP residues 455-912 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase | ||
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#2: Protein | Mass: 24119.654 Da / Num. of mol.: 1 / Fragment: UNP residues 178-379 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | #4: Chemical | ChemComp-SAH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.6 / Details: 0.05M Bis-Tris, 0.1M Sodium Malonate, 8% PEG3350 / PH range: 5.6-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2816 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 5.7 % / Number: 80080 / Rmerge(I) obs: 0.098 / Χ2: 0.88 / D res high: 3.82 Å / D res low: 50 Å / Num. obs: 14153 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 3.82→50 Å / Num. obs: 14153 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.31 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.046 / Rrim(I) all: 0.108 / Χ2: 0.885 / Net I/av σ(I): 13.222 / Net I/σ(I): 6.9 / Num. measured all: 80080 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QRV, 3A1A Resolution: 3.821→42.005 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.85 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 431.61 Å2 / Biso mean: 78.3298 Å2 / Biso min: 0 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.821→42.005 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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