|Entry||Database: EMDB / ID: EMD-30454|
|Title||NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (class2 map)|
|Sample||NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (class2 map):|
187-bp NCP / NSD3
|Biological species||Xenopus laevis (African clawed frog) / Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.24 Å|
|Authors||Li W / Tian W / Yuan G / Deng P / Gozani O / Patel D / Wang Z|
|Funding support|| China, United States, 6 items |
|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.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_30454.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.08 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp N...
|Entire||Name: NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (class2 map)|
Number of components: 3
-Component #1: protein, NSD3 bearing E1181K/T1232A dual mutation in complex with...
|Protein||Name: NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (class2 map)|
Recombinant expression: No
|Mass||Experimental: 300 kDa|
-Component #2: protein, 187-bp NCP
|Protein||Name: 187-bp NCP / Recombinant expression: No|
|Source||Species: Xenopus laevis (African clawed frog)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
-Component #3: protein, NSD3
|Protein||Name: NSD3 / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Baculovirus transfer vector pFASTBAC1|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.3 mg/mL / pH: 7.5|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Bioquantum|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 132902|
|3D reconstruction||Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF|
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