7CRQ

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.

Li, W.Tian, W.Yuan, G.Deng, P.Sengupta, D.Cheng, Z.Cao, Y.Ren, J.Qin, Y.Zhou, Y.Jia, Y.Gozani, O.Patel, D.J.Wang, Z.

(2021) Nature 590: 498-503

  • DOI: 10.1038/s41586-020-03069-8
  • Primary Citation of Related Structures:  
    7CRP, 7CRQ, 7CRO, 7CRR

  • PubMed 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 1,2 . NSD enzymes exhibit an autoinhibitory state that is relieved by binding to nucleosomes, enabling dimethylation of histone H3 at Lys36 (H3K36) 3-7 ...

    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 1,2 . NSD enzymes exhibit an autoinhibitory state that is relieved by binding to nucleosomes, enabling dimethylation of histone H3 at Lys36 (H3K36) 3-7 . 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.


    Organizational Affiliation

    Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China. wangz@bnu.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3E, A [auth M]135Xenopus laevisMutation(s): 3 
Gene Names: h3c8.Sh3c8H3lhist1h3g
UniProt
Find proteins for Q92133 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BD, H122Xenopus tropicalisMutation(s): 0 
Gene Names: h2bc12hist1h2bk
UniProt
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD3K [auth I], L758Homo sapiensMutation(s): 2 
Gene Names: NSD3WHSC1L1DC28
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZ95 (Homo sapiens)
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PHAROS:  Q9BZ95
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (168-MER)I [auth A]187Xenopus laevis
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (168-MER)J [auth K]187Xenopus laevis
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Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
A [auth M], EL-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870725
National Natural Science Foundation of China (NSFC)China31570729
Other governmentChinaFundamental Research Funds for the Central Universities (2017EYT19)
Other governmentUnited StatesMemorial Sloan-Kettering Cancer Center Core grant P30CA008748
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesR01GM079641
Other governmentChinaBasic Research grant from Shenzhen government (JCYJ20180302174213122)

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-01-13
    Changes: Database references
  • Version 2.0: 2021-01-20
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2021-03-03
    Changes: Database references