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Yorodumi- EMDB-20281: The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20281 | |||||||||
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Title | The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. | |||||||||
Map data | The cryo-EM map of human DNMT3A2/3B3 with NCP. | |||||||||
Sample |
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Keywords | methyltransferase / complex / TRANSFERASE / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information : / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / : / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase ...: / positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / : / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / XY body / DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / cellular response to ethanol / response to vitamin A / : / response to ionizing radiation / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / response to cocaine / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to amino acid stimulus / response to lead ion / euchromatin / NoRC negatively regulates rRNA expression / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / structural constituent of chromatin / transcription corepressor activity / nucleosome / response to estradiol / cellular response to hypoxia / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / synthetic construct (others) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.94 Å | |||||||||
Authors | Xu TH / Liu M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2020 Title: Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Authors: Ting-Hai Xu / Minmin Liu / X Edward Zhou / Gangning Liang / Gongpu Zhao / H Eric Xu / Karsten Melcher / Peter A Jones / Abstract: CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially ...CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core, and they favour the methylation of linker DNA at positioned nucleosomes. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20281.map.gz | 6.7 MB | EMDB map data format | |
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Header (meta data) | emd-20281-v30.xml emd-20281.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
Images | emd_20281.png | 45.6 KB | ||
Filedesc metadata | emd-20281.cif.gz | 7.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20281 | HTTPS FTP |
-Related structure data
Related structure data | 6pa7MC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20281.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The cryo-EM map of human DNMT3A2/3B3 with NCP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.029 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes
+Supramolecule #1: A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes
+Supramolecule #2: Histone
+Supramolecule #3: DNA (167-MER)
+Supramolecule #4: DNA (cytosine-5)-methyltransferase
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: DNA (cytosine-5)-methyltransferase 3A
+Macromolecule #8: DNA (cytosine-5)-methyltransferase 3B
+Macromolecule #5: DNA (167-MER)
+Macromolecule #6: DNA (167-MER)
+Macromolecule #9: CHLORIDE ION
+Macromolecule #10: S-ADENOSYL-L-HOMOCYSTEINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 |
Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 65.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 2190114 |
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Startup model | Type of model: OTHER |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 599344 |