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Yorodumi- PDB-8te3: Crystal structure of the methyltransferase domain of R882C/R676K ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8te3 | ||||||
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Title | Crystal structure of the methyltransferase domain of R882C/R676K DNMT3A homotetramer | ||||||
Components | DNA (cytosine-5)-methyltransferase 3A | ||||||
Keywords | TRANSFERASE / DNA methyltransferase | ||||||
Function / homology | Function and homology information positive regulation of cellular response to hypoxia / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins ...positive regulation of cellular response to hypoxia / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / XY body / cellular response to ethanol / response to vitamin A / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / cellular response to amino acid stimulus / response to lead ion / euchromatin / 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 / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Lu, J.W. / Song, J.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the homo-tetrameric DNMT3A methyltransferase domain(R882C/R676K) Authors: Lu, J.W. / Song, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8te3.cif.gz | 360.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8te3.ent.gz | 289.7 KB | Display | PDB format |
PDBx/mmJSON format | 8te3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8te3_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8te3_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8te3_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 8te3_validation.cif.gz | 78.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/8te3 ftp://data.pdbj.org/pub/pdb/validation_reports/te/8te3 | HTTPS FTP |
-Related structure data
Related structure data | 5yx2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32777.773 Da / Num. of mol.: 8 / Fragment: methyltransferase domain (UNP residues 628-912) / Mutation: R882C,R676K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-SAH / 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: 3.83 Å3/Da / Density % sol: 67.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2-0.4 M potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 64344 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 63.07 Å2 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.161 / Rrim(I) all: 0.334 / Χ2: 0.674 / Net I/σ(I): 2.5 / Num. measured all: 273938 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5YX2 Resolution: 3.2→46.96 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.8 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 179.67 Å2 / Biso mean: 56.5082 Å2 / Biso min: 17.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→46.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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