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- PDB-6u90: Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u90 | ||||||
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Title | Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA | ||||||
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![]() | Transferase/DNA / DNMT3B / DNMT3L / DNA methylation / Methyltransferase / transferase-DNA complex / TRANSFERASE | ||||||
Function / homology | ![]() 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 / 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 / PRC2 methylates histones and DNA / Defective pyroptosis / stem cell differentiation / NoRC negatively regulates rRNA expression / placenta development / transcription corepressor activity / spermatogenesis / methylation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, L. / Song, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms Authors: Gao, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.6 KB | Display | ![]() |
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PDB format | ![]() | 182.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6u91C ![]() 5yx2S 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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Unit cell |
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Components
-DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules ADBC
#1: Protein | Mass: 33143.391 Da / Num. of mol.: 2 / Mutation: N779A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UBC3, 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.) ![]() ![]() ![]() |
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-DNA chain , 1 types, 2 molecules EF
#3: DNA chain | Mass: 7698.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 25 molecules ![](data/chem/img/GOL.gif)
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![](data/chem/img/HOH.gif)
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.54 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2018 |
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→47.8765 Å / Num. obs: 40636 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 67.3761830965 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.52 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.984 / Num. unique obs: 4056 / CC1/2: 0.858 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YX2 Resolution: 3.00081756367→47.8765 Å / SU ML: 0.486596651553 / Cross valid method: FREE R-VALUE / σ(F): 1.97481947278 / Phase error: 28.5011384388 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 87.9542643825 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.00081756367→47.8765 Å
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Refine LS restraints |
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LS refinement shell |
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