+Open data
-Basic information
Entry | Database: PDB / ID: 4u7t | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of DNMT3A-DNMT3L in complex with histone H3 | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/TRANSFERASE REGULATOR / DNA methyltransferase / active form / TRANSFERASE-TRANSFERASE REGULATOR complex | ||||||
Function / homology | Function and homology information retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / protein-cysteine methyltransferase activity / negative regulation of chromosome condensation / genomic imprinting ...retrotransposon silencing by heterochromatin formation / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / protein-cysteine methyltransferase activity / negative regulation of chromosome condensation / genomic imprinting / Barr body / regulation of centromere complex assembly / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / muscle cell differentiation / negative regulation of DNA methylation-dependent heterochromatin formation / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / pericentric heterochromatin formation / inner kinetochore / ESC/E(Z) complex / XY body / response to vitamin A / cellular response to ethanol / DNA methylation-dependent heterochromatin formation / lncRNA binding / oocyte maturation / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / negative regulation of gene expression, epigenetic / nucleus organization / hepatocyte apoptotic process / male meiosis I / chromosome, centromeric region / catalytic complex / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / nucleosomal DNA binding / enzyme activator activity / Inhibition of DNA recombination at telomere / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / condensed nuclear chromosome / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / stem cell differentiation / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / cellular response to amino acid stimulus / response to lead ion / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / placenta development / multicellular organism growth / B-WICH complex positively regulates rRNA expression / neuron differentiation / response to toxic substance / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / male gonad development / nucleosome / nucleosome assembly / response to estradiol / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / spermatogenesis / Oxidative Stress Induced Senescence / methylation / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / chromosome, telomeric region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | ||||||
Authors | Guo, X. / Wang, L. / Yin, X. / Li, J. / Xiao, J. / He, S. / Wang, J. / Xu, Y. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Structural insight into autoinhibition and histone H3-induced activation of DNMT3A Authors: Guo, X. / Wang, L. / Li, J. / Ding, Z. / Xiao, J. / Yin, X. / He, S. / Shi, P. / Dong, L. / Li, G. / Tian, C. / Wang, J. / Cong, Y. / Xu, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4u7t.cif.gz | 265.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4u7t.ent.gz | 210.2 KB | Display | PDB format |
PDBx/mmJSON format | 4u7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/4u7t ftp://data.pdbj.org/pub/pdb/validation_reports/u7/4u7t | HTTPS FTP |
---|
-Related structure data
Related structure data | 4u7pC 2qrvS 3a1aS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | biological unit is the same as asym. |
-Components
-DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 50878.434 Da / Num. of mol.: 2 / Fragment: UNP residues 476-912 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase #2: Protein | Mass: 24119.654 Da / Num. of mol.: 2 / Fragment: UNP residues 178-379 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 |
---|
-Protein/peptide , 1 types, 2 molecules FG
#3: Protein/peptide | Mass: 1308.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243 |
---|
-Non-polymers , 3 types, 19 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.37 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium Acetate, 0.6M Ammonium Sulfate / PH range: 5.3-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 9.9 % / Number: 519306 / Rmerge(I) obs: 0.095 / Χ2: 1.06 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 52477 / % possible obs: 99.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 52477 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 77.28 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 139.3 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A1A, 2QRV Resolution: 2.9→40.213 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.49 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 199.66 Å2 / Biso mean: 83.463 Å2 / Biso min: 34.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→40.213 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
|