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 

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:  

  • 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. W ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE HISTONE-BINDING PROTEIN CAF1
A, B
422Drosophila melanogasterMutation(s): 0 
Gene Names: Caf1
Find proteins for Q24572 (Drosophila melanogaster)
Go to UniProtKB:  Q24572
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3
C, D
19Drosophila melanogasterMutation(s): 0 
Gene Names: His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Find proteins for P02299 (Drosophila melanogaster)
Go to UniProtKB:  P02299
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.980α = 90.00
b = 88.160β = 90.00
c = 204.070γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
SCALAdata scaling
BUSTERrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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