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Yorodumi- EMDB-30453: NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30453 | |||||||||||||||||||||
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Title | NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / regulation of double-strand break repair via nonhomologous end joining / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / atrial septum primum morphogenesis / membranous septum morphogenesis ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / regulation of double-strand break repair via nonhomologous end joining / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / atrial septum primum morphogenesis / membranous septum morphogenesis / histone H3K36 methyltransferase activity / histone H3 methyltransferase activity / Nonhomologous End-Joining (NHEJ) / bone development / G2/M DNA damage checkpoint / PKMTs methylate histone lysines / structural constituent of chromatin / double-strand break repair / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / methylation / Processing of DNA double-strand break ends / sequence-specific DNA binding / protein heterodimerization activity / chromatin binding / chromatin / nucleolus / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Xenopus laevis (African clawed frog) / Homo sapiens (human) / Xenopus tropicalis (tropical clawed frog) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||||||||||||||
Authors | Li W / Tian W / Yuan G / Deng P / Gozani O / Patel D / Wang Z | |||||||||||||||||||||
Funding support | China, United States, 6 items
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Citation | Journal: Nature / Year: 2021 Title: Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases. Authors: Wanqiu Li / Wei Tian / Gang Yuan / Pujuan Deng / Deepanwita Sengupta / Zhongjun Cheng / Yinghua Cao / Jiahao Ren / Yan Qin / Yuqiao Zhou / Yulin Jia / Or Gozani / Dinshaw J Patel / Zhanxin Wang / Abstract: Histone methyltransferases of the nuclear receptor-binding SET domain protein (NSD) family, including NSD1, NSD2 and NSD3, have crucial roles in chromatin regulation and are implicated in oncogenesis. ...Histone methyltransferases of the nuclear receptor-binding SET domain protein (NSD) family, including NSD1, NSD2 and NSD3, have crucial roles in chromatin regulation and are implicated in oncogenesis. NSD enzymes exhibit an autoinhibitory state that is relieved by binding to nucleosomes, enabling dimethylation of histone H3 at Lys36 (H3K36). However, the molecular basis that underlies this mechanism is largely unknown. Here we solve the cryo-electron microscopy structures of NSD2 and NSD3 bound to mononucleosomes. We find that binding of NSD2 and NSD3 to mononucleosomes causes DNA near the linker region to unwrap, which facilitates insertion of the catalytic core between the histone octamer and the unwrapped segment of DNA. A network of DNA- and histone-specific contacts between NSD2 or NSD3 and the nucleosome precisely defines the position of the enzyme on the nucleosome, explaining the specificity of methylation to H3K36. Intermolecular contacts between NSD proteins and nucleosomes are altered by several recurrent cancer-associated mutations in NSD2 and NSD3. NSDs that contain these mutations are catalytically hyperactive in vitro and in cells, and their ectopic expression promotes the proliferation of cancer cells and the growth of xenograft tumours. Together, our research provides molecular insights into the nucleosome-based recognition and histone-modification mechanisms of NSD2 and NSD3, which could lead to strategies for therapeutic targeting of proteins of the NSD family. | |||||||||||||||||||||
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_30453.map.gz | 35 MB | EMDB map data format | |
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Header (meta data) | emd-30453-v30.xml emd-30453.xml | 23 KB 23 KB | Display Display | EMDB header |
Images | emd_30453.png | 134.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30453 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30453 | HTTPS FTP |
-Related structure data
Related structure data | 7croMC 7crpC 7crqC 7crrC M: atomic model generated by this map C: citing same article (ref.) |
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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_30453.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 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 : NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP
+Supramolecule #1: NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP
+Supramolecule #2: Histone H3, H4, H2A and H2B
+Supramolecule #3: DNA
+Supramolecule #4: NSD2
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B
+Macromolecule #7: Histone-lysine N-methyltransferase NSD2
+Macromolecule #5: DNA (168-MER)
+Macromolecule #6: DNA (168-MER)
+Macromolecule #8: S-ADENOSYLMETHIONINE
+Macromolecule #9: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV Details: blotted for 3 s before being plunged into liquid ethane. |
Details | The sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71116 |