3H6Z

Crystal Structure of the Four MBT Repeats of Drosophila melanogaster Sfmbt in Complex with Peptide RHR (me)K VLR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt

Grimm, C.Matos, R.Ly-Hartig, N.Steuerwald, U.Lindner, D.Rybin, V.Muller, J.Muller, C.W.

(2009) Embo J. 28: 1965-1977

  • DOI: 10.1038/emboj.2009.147

  • PubMed Abstract: 
  • Polycomb group (PcG) proteins repress transcription by modifying chromatin structure in target genes. dSfmbt is a subunit of the Drosophila melanogaster PcG protein complex PhoRC and contains four malignant brain tumour (MBT) repeats involved in the ...

    Polycomb group (PcG) proteins repress transcription by modifying chromatin structure in target genes. dSfmbt is a subunit of the Drosophila melanogaster PcG protein complex PhoRC and contains four malignant brain tumour (MBT) repeats involved in the recognition of various mono- and dimethylated histone peptides. Here, we present the crystal structure of the four-MBT-repeat domain of dSfmbt in complex with a mono-methylated histone H4 peptide. Only a single histone peptide binds to the four-MBT-repeat domain. Mutational analyses show high-affinity binding with low peptide sequence selectivity through combinatorial interaction of the methyl-lysine with an aromatic cage and positively charged flanking residues with the surrounding negatively charged surface of the fourth MBT repeat. dSfmbt directly interacts with the PcG protein Scm, a related MBT-repeat protein with similar methyl-lysine binding activity. dSfmbt and Scm co-occupy Polycomb response elements of target genes in Drosophila and they strongly synergize in the repression of these target genes, suggesting that the combined action of these two MBT proteins is crucial for Polycomb silencing.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein Sfmbt
A, B
447Drosophila melanogasterMutation(s): 3 
Gene Names: Sfmbt
Find proteins for Q9VK33 (Drosophila melanogaster)
Go to UniProtKB:  Q9VK33
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
'HR(MLZ)VLR
L, M
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A, B
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
L, M
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.800α = 90.00
b = 97.040β = 90.00
c = 214.120γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
ADSCdata collection
XSCALEdata scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance