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Yorodumi- PDB-6u90: Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u90 | ||||||
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Title | Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT 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: 3.00081756367 Å | ||||||
Authors | Gao, L. / Song, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u90.cif.gz | 239.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u90.ent.gz | 182.3 KB | Display | PDB format |
PDBx/mmJSON format | 6u90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u90_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6u90_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6u90_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 6u90_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/6u90 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/6u90 | HTTPS FTP |
-Related structure data
Related structure data | 6u91C 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: 33143.391 Da / Num. of mol.: 2 / Mutation: N779A 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, 25 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: 4.04 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: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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