+Open data
-Basic information
Entry | Database: PDB / ID: 6u8p | ||||||
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Title | Crystal structure of DNMT3B-DNMT3L in complex with CpGpA DNA | ||||||
Components |
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Keywords | Transferase/DNA / DNMT3B / DNMT3L / DNA methylation / Methyltransferase / transferase-DNA complex / TRANSFERASE | ||||||
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 / 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 / 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 / NoRC negatively regulates rRNA expression / placenta development / transcription corepressor activity / methylation / spermatogenesis / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Gao, L. / Song, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Authors: Gao, L. / Emperle, M. / Guo, Y. / Grimm, S.A. / Ren, W. / Adam, S. / Uryu, H. / Zhang, Z.M. / Chen, D. / Yin, J. / Dukatz, M. / Anteneh, H. / Jurkowska, R.Z. / Lu, J. / Wang, Y. / ...Authors: Gao, L. / Emperle, M. / Guo, Y. / Grimm, S.A. / Ren, W. / Adam, S. / Uryu, H. / Zhang, Z.M. / Chen, D. / Yin, J. / Dukatz, M. / Anteneh, H. / Jurkowska, R.Z. / Lu, J. / Wang, Y. / Bashtrykov, P. / Wade, P.A. / Wang, G.G. / Jeltsch, A. / Song, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u8p.cif.gz | 283.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u8p.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 6u8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u8p_validation.pdf.gz | 1012.5 KB | Display | wwPDB validaton report |
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Full document | 6u8p_full_validation.pdf.gz | 1023.4 KB | Display | |
Data in XML | 6u8p_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 6u8p_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/6u8p ftp://data.pdbj.org/pub/pdb/validation_reports/u8/6u8p | HTTPS FTP |
-Related structure data
Related structure data | 6u8vC 6u8wC 6u8xC 5yx2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules ADBC
#1: Protein | Mass: 33186.414 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) / Variant (production host): DE3 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.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli (E. coli) / Variant (production host): DE3 / References: UniProt: Q9UJW3 |
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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.) Homo sapiens (human) |
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-Non-polymers , 3 types, 42 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.29 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl (pH 8.0), 100 mM MgCl2, 7% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 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: 3.04308940064→50 Å / Num. obs: 39794 / % possible obs: 100 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.071 / Rrim(I) all: 0.149 / Χ2: 0.641 / Net I/σ(I): 4.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YX2 Resolution: 3.05→48.32575 Å / SU ML: 0.363351429439 / Cross valid method: FREE R-VALUE / σ(F): 1.97543196468 / Phase error: 25.0083282289
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.6118931347 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→48.32575 Å
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Refine LS restraints |
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LS refinement shell |
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