+Open data
-Basic information
Entry | Database: PDB / ID: 7x9d | ||||||
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Title | DNMT3B in complex with harmine | ||||||
Components |
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Keywords | TRANSFERASE / Inhibitor / Comple / Methyltransferase | ||||||
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 ...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 / placenta development / NoRC negatively regulates rRNA expression / transcription corepressor activity / methylation / spermatogenesis / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | ||||||
Authors | Cho, C.-C. / Yuan, H.S. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Mechanistic Insights into Harmine-Mediated Inhibition of Human DNA Methyltransferases and Prostate Cancer Cell Growth. Authors: Cho, C.C. / Lin, C.J. / Huang, H.H. / Yang, W.Z. / Fei, C.Y. / Lin, H.Y. / Lee, M.S. / 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 | 7x9d.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x9d.ent.gz | 159 KB | Display | PDB format |
PDBx/mmJSON format | 7x9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/7x9d ftp://data.pdbj.org/pub/pdb/validation_reports/x9/7x9d | HTTPS FTP |
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-Related structure data
Related structure data | 6kdpS 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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Unit cell |
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-Components
#1: Protein | Mass: 32715.859 Da / Num. of mol.: 2 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 | 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: 4.51 Å3/Da / Density % sol: 72.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: bis-tris propane pH 7.0, sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.08→30 Å / Num. obs: 35934 / % possible obs: 97.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 67.42 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.042 / Rrim(I) all: 0.095 / Χ2: 0.886 / Net I/σ(I): 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KDP Resolution: 3.08→29.94 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.59 / 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: 157.7 Å2 / Biso mean: 62.7657 Å2 / Biso min: 18.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.08→29.94 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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