6PA7

The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B.

Xu, T.H.Liu, M.Zhou, X.E.Liang, G.Zhao, G.Xu, H.E.Melcher, K.Jones, P.A.

(2020) Nature 586: 151-155

  • DOI: 10.1038/s41586-020-2747-1
  • Primary Citation of Related Structures:  
    6PA7

  • PubMed Abstract: 
  • CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer 1 . These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core 2 , and they favour the methylation of linker DNA at positioned nucleosomes 3,4 ...

    CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer 1 . These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core 2 , and they favour the methylation of linker DNA at positioned nucleosomes 3,4 . Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.


    Organizational Affiliation

    Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA. peter.jones@vai.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2A, E135Xenopus laevisMutation(s): 0 
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Find proteins for P84233 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F103Xenopus laevisMutation(s): 0 
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Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1C, G129Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H123Xenopus laevisMutation(s): 1 
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Find proteins for P02281 (Xenopus laevis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3AK, M [auth P]689Homo sapiensMutation(s): 0 
Gene Names: DNMT3A
EC: 2.1.1.37
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Find proteins for Q9Y6K1 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3BL [auth N], N [auth S]770Homo sapiensMutation(s): 0 
Gene Names: DNMT3B
EC: 2.1.1.37
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Find proteins for Q9UBC3 (Homo sapiens)
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PHAROS:  Q9UBC3
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Entity ID: 5
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DNA (167-MER)I167synthetic construct
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Entity ID: 6
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DNA (167-MER)J167synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR35CA209859

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2020-10-14
    Changes: Database references