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Yorodumi- EMDB-72318: Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer b... -
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Basic information
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| Title | Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome | |||||||||
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Keywords | DNMT3A2-DNMT3B3 / DNA methylation / 167H3K36me2-nucleosome / DNA BINDING PROTEIN | |||||||||
| Function / homology | Function and homology informationDNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / transposable element silencing by piRNA-mediated DNA methylation / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia / DNA-methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / hepatocyte apoptotic process ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / transposable element silencing by piRNA-mediated DNA methylation / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia / DNA-methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / hepatocyte apoptotic process / response to vitamin A / XY body / SUMOylation of DNA methylation proteins / DNA methylation-dependent constitutive heterochromatin formation / cellular response to ethanol / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / lncRNA binding / chromosome, centromeric region / catalytic complex / heterochromatin / methylation / Transferases; Transferring one-carbon groups; Methyltransferases / response to cocaine / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / euchromatin / response to toxic substance / NoRC negatively regulates rRNA expression / response to lead ion / nucleosomal DNA binding / nuclear matrix / RMTs methylate histone arginines / innate immune response in mucosa / transcription corepressor activity / response to estradiol / structural constituent of chromatin / neuron differentiation / nucleosome / nucleosome assembly / chromatin organization / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / antibacterial humoral response / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromosome / 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 / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Xie X / Zhou XE / Worden EJ / Jones PA | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2026Title: Nucleosome spacing regulates linker methylation by DNMT3A2/3B3. Authors: Xiaoyan Xie / Minmin Liu / Gabriella N L Chua / X Edward Zhou / Michelle L Dykstra / Shixin Liu / Peter A Jones / Evan J Worden / ![]() Abstract: De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get ...De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get targeted by DNMT3 enzymes are not understood. We show that nucleosome spacing controls linker DNA methylation and H3K36me2 recognition by human DNMT3A2/3B3, linking de novo methylation to chromatin architecture. We present structures of DNMT3A2/3B3 bound to dinucleosomes, revealing that short linkers promote dinucleosome bridging, blocking access to linker DNA and suppressing methylation, whereas long linkers allow DNMT3A2/3B3 to engage each nucleosome separately and methylate linker DNA. Finally, we show that DNMT3A2/3B3 positions proline-tryptophan-tryptophan-proline (PWWP) domains to scan for H3K36me2. However, H3K36me2 recognition is blocked when DNMT3A2/3B3 bridges dinucleosomes with short linkers, imposing an additional structural constraint on DNMT3A2/3B3 function. Together, these findings uncover the mechanisms that govern de novo methylation in chromatin and explain how DNMT3 enzymes target linkers in cells. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_72318.map.gz | 17.2 MB | EMDB map data format | |
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| Header (meta data) | emd-72318-v30.xml emd-72318.xml | 27.7 KB 27.7 KB | Display Display | EMDB header |
| Images | emd_72318.png | 52.4 KB | ||
| Filedesc metadata | emd-72318.cif.gz | 7.9 KB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-72318 ftp://data.pdbj.org/pub/emdb/structures/EMD-72318 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9q7uMC ![]() 9e00C ![]() 9e05C ![]() 9e09C ![]() 9e0fC ![]() 9e0gC ![]() 9e0rC ![]() 9e2dC ![]() 9e2fC ![]() 9e2qC ![]() 9e2rC ![]() 9e3dC ![]() 9e3rC ![]() 9e49C ![]() 9y4pC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_72318.map.gz / Format: CCP4 / Size: 57.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.656 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : DNMT3A/3B tetramer bound to 167H3K36me2-nucleosome
+Supramolecule #1: DNMT3A/3B tetramer bound to 167H3K36me2-nucleosome
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Isoform 7 of DNA (cytosine-5)-methyltransferase 3B
+Macromolecule #8: DNA (cytosine-5)-methyltransferase 3A
+Macromolecule #5: DNA (162-MER)
+Macromolecule #6: DNA (162-MER)
+Macromolecule #9: ZINC ION
+Macromolecule #10: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.8 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 1 items
Citation











































Z (Sec.)
Y (Row.)
X (Col.)





















Spodoptera (butterflies/moths)
Processing
FIELD EMISSION GUN

