7E8D

NSD2 E1099K mutant bound to nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2.

Sato, K.Kumar, A.Hamada, K.Okada, C.Oguni, A.Machiyama, A.Sakuraba, S.Nishizawa, T.Nureki, O.Kono, H.Ogata, K.Sengoku, T.

(2021) Nat Commun 12: 6605-6605

  • DOI: https://doi.org/10.1038/s41467-021-26913-5
  • Primary Citation of Related Structures:  
    7E8D

  • PubMed Abstract: 

    Dimethylated histone H3 Lys36 (H3K36me2) regulates gene expression, and aberrant H3K36me2 upregulation, resulting from either the overexpression or point mutation of the dimethyltransferase NSD2, is found in various cancers. Here we report the cryo-electron microscopy structure of NSD2 bound to the nucleosome. Nucleosomal DNA is partially unwrapped, facilitating NSD2 access to H3K36. NSD2 interacts with DNA and H2A along with H3. The NSD2 autoinhibitory loop changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed that two oncogenic mutations, E1099K and T1150A, increase NSD2 catalytic turnover. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild-type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing catalytic turnover. Our analyses guide the development of specific inhibitors of NSD2.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
135Homo sapiensMutation(s): 1 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
129Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P0C0S8 (Homo sapiens)
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PHAROS:  P0C0S8
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UniProt GroupP0C0S8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
125Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
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GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD2254Homo sapiensMutation(s): 1 
Gene Names: NSD2KIAA1090MMSETTRX5WHSC1
EC: 2.1.1.357
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Find proteins for O96028 (Homo sapiens)
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PHAROS:  O96028
GTEx:  ENSG00000109685 
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UniProt GroupO96028
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (185-MER)185synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (185-MER)185synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references