2YBA

Crystal structure of Nurf55 in complex with histone H3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Histone Methylation by Prc2 is Inhibited by Active Chromatin Marks

Schmitges, F.W.Prusty, A.B.Faty, M.Stutzer, A.Lingaraju, G.M.Aiwazian, J.Sack, R.Hess, D.Li, L.Zhou, S.Bunker, R.D.Wirth, U.Bouwmeester, T.Bauer, A.Ly-Hartig, N.Zhao, K.Chan, H.Gu, J.Gut, H.Fischle, W.Muller, J.Thoma, N.H.

(2011) Mol Cell 42: 330

  • DOI: 10.1016/j.molcel.2011.03.025
  • Primary Citation of Related Structures:  
    2YB8, 2YBA

  • PubMed Abstract: 
  • The Polycomb repressive complex 2 (PRC2) confers transcriptional repression through histone H3 lysine 27 trimethylation (H3K27me3). Here, we examined how PRC2 is modulated by histone modifications associated with transcriptionally active chromatin. We provide the molecular basis of histone H3 N terminus recognition by the PRC2 Nurf55-Su(z)12 submodule ...

    The Polycomb repressive complex 2 (PRC2) confers transcriptional repression through histone H3 lysine 27 trimethylation (H3K27me3). Here, we examined how PRC2 is modulated by histone modifications associated with transcriptionally active chromatin. We provide the molecular basis of histone H3 N terminus recognition by the PRC2 Nurf55-Su(z)12 submodule. Binding of H3 is lost if lysine 4 in H3 is trimethylated. We find that H3K4me3 inhibits PRC2 activity in an allosteric fashion assisted by the Su(z)12 C terminus. In addition to H3K4me3, PRC2 is inhibited by H3K36me2/3 (i.e., both H3K36me2 and H3K36me3). Direct PRC2 inhibition by H3K4me3 and H3K36me2/3 active marks is conserved in humans, mouse, and fly, rendering transcriptionally active chromatin refractory to PRC2 H3K27 trimethylation. While inhibition is present in plant PRC2, it can be modulated through exchange of the Su(z)12 subunit. Inhibition by active chromatin marks, coupled to stimulation by transcriptionally repressive H3K27me3, enables PRC2 to autonomously template repressive H3K27me3 without overwriting active chromatin domains.


    Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE HISTONE-BINDING PROTEIN CAF1A, B422Drosophila melanogasterMutation(s): 0 
Gene Names: Caf1-55Caf1CG4236
UniProt
Find proteins for Q24572 (Drosophila melanogaster)
Explore Q24572 
Go to UniProtKB:  Q24572
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE H3C, D19Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P02299 (Drosophila melanogaster)
Explore P02299 
Go to UniProtKB:  P02299
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.98α = 90
b = 88.16β = 90
c = 204.07γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-05-12
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy