4A7J

Symmetric Dimethylation of H3 Arginine 2 is a Novel Histone Mark that Supports Euchromatin Maintenance


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Symmetric Dimethylation of H3R2 is a Newly Identified Histone Mark that Supports Euchromatin Maintenance

Migliori, V.Muller, J.Phalke, S.Low, D.Bezzi, M.Chuenmok, W.Sahu, S.K.Gunaratne, J.Capasso, P.Bassi, C.Cecatiello, V.Demarco, A.Blackstock, W.Kuznetsov, V.Amati, B.Mapelli, M.Guccione, E.

(2012) Nat.Struct.Mol.Biol. 19: 136

  • DOI: 10.1038/nsmb.2209

  • PubMed Abstract: 
  • The asymmetric dimethylation of histone H3 arginine 2 (H3R2me2a) acts as a repressive mark that antagonizes trimethylation of H3 lysine 4. Here we report that H3R2 is also symmetrically dimethylated (H3R2me2s) by PRMT5 and PRMT7 and present in euchro ...

    The asymmetric dimethylation of histone H3 arginine 2 (H3R2me2a) acts as a repressive mark that antagonizes trimethylation of H3 lysine 4. Here we report that H3R2 is also symmetrically dimethylated (H3R2me2s) by PRMT5 and PRMT7 and present in euchromatic regions. Profiling of H3-tail interactors by SILAC MS revealed that H3R2me2s excludes binding of RBBP7, a central component of co-repressor complexes Sin3a, NURD and PRC2. Conversely H3R2me2s enhances binding of WDR5, a common component of the coactivator complexes MLL, SET1A, SET1B, NLS1 and ATAC. The interaction of histone H3 with WDR5 distinguishes H3R2me2s from H3R2me2a, which impedes the recruitment of WDR5 to chromatin. The crystallographic structure of WDR5 and the H3R2me2s peptide elucidates the molecular determinants of this high affinity interaction. Our findings identify H3R2me2s as a previously unknown mark that keeps genes poised in euchromatin for transcriptional activation upon cell-cycle withdrawal and differentiation in human cells.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD REPEAT-CONTAINING PROTEIN 5
A
318Homo sapiensMutation(s): 0 
Gene Names: WDR5 (BIG3)
Find proteins for P61964 (Homo sapiens)
Go to Gene View: WDR5
Go to UniProtKB:  P61964
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3.1T
B
16Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2MR
Query on 2MR
B
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.600α = 90.00
b = 46.800β = 104.33
c = 65.000γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2012-02-15
    Type: Other