5CIU

Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report



Literature

Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B.

Rondelet, G.Dal Maso, T.Willems, L.Wouters, J.

(2016) J Struct Biol 194: 357-367

  • DOI: 10.1016/j.jsb.2016.03.013
  • Primary Citation of Related Structures:  
    5CIU, 5CIY

  • PubMed Abstract: 
  • DNA methylation is an important epigenetic modification involved in chromatin organization and gene expression. The function of DNA methylation depends on cell context and is correlated with histone modification patterns. In particular, trimethylatio ...

    DNA methylation is an important epigenetic modification involved in chromatin organization and gene expression. The function of DNA methylation depends on cell context and is correlated with histone modification patterns. In particular, trimethylation of Lys36 on histone H3 tail (H3K36me3) is associated with DNA methylation and elongation phase of transcription. PWWP domains of the de novo DNA methyltransferases DNMT3A and DNMT3B read this epigenetic mark to guide DNA methylation. Here we report the first crystal structure of the DNMT3B PWWP domain-H3K36me3 complex. Based on this structure, we propose a model of the DNMT3A PWWP domain-H3K36me3 complex and build a model of DNMT3A (PWWP-ADD-CD) in a nucleosomal context. The trimethylated side chain of Lys36 (H3K36me3) is inserted into an aromatic cage similar to the "Royal" superfamily domains known to bind methylated histones. A key interaction between trimethylated Lys36 and a conserved water molecule stabilized by Ser270 explains the lack of affinity of mutated DNMT3B (S270P) for the H3K36me3 epigenetic mark in the ICF (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome. The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome highlights the mechanism for recognition of nucleosome by DNMT3s and explains the periodicity of de novo DNA methylation.


    Organizational Affiliation

    Department of Chemistry, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3BAB150Homo sapiensMutation(s): 0 
Gene Names: DNMT3B
EC: 2.1.1.37
Find proteins for Q9UBC3 (Homo sapiens)
Explore Q9UBC3 
Go to UniProtKB:  Q9UBC3
NIH Common Fund Data Resources
PHAROS  Q9UBC3
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2CD15Homo sapiensMutation(s): 0 
Gene Names: H3C15HIST2H3AH3C14H3F2H3FMHIST2H3CH3C13HIST2H3D
Find proteins for Q71DI3 (Homo sapiens)
Explore Q71DI3 
Go to UniProtKB:  Q71DI3
NIH Common Fund Data Resources
PHAROS  Q71DI3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
C,DL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.437α = 90
b = 73.437β = 90
c = 158.2γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 2.0: 2019-06-12
    Changes: Advisory, Atomic model, Data collection, Structure summary