1PDQ

Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains

Fischle, W.Wang, Y.Jacobs, S.A.Kim, Y.Allis, C.D.Khorasanizadeh, S.

(2003) Genes Dev. 17: 1870-1881

  • DOI: 10.1101/gad.1110503

  • PubMed Abstract: 
  • On the histone H3 tail, Lys 9 and Lys 27 are both methylation sites associated with epigenetic repression, and reside within a highly related sequence motif ARKS. Here we show that the chromodomain proteins Polycomb (Pc) and HP1 (heterochromatin prot ...

    On the histone H3 tail, Lys 9 and Lys 27 are both methylation sites associated with epigenetic repression, and reside within a highly related sequence motif ARKS. Here we show that the chromodomain proteins Polycomb (Pc) and HP1 (heterochromatin protein 1) are highly discriminatory for binding to these sites in vivo and in vitro. In Drosophila S2 cells, and on polytene chromosomes, methyl-Lys 27 and Pc are both excluded from areas that are enriched in methyl-Lys 9 and HP1. Swapping of the chromodomain regions of Pc and HP1 is sufficient for switching the nuclear localization patterns of these factors, indicating a role for their chromodomains in both target site binding and discrimination. To better understand the molecular basis for the selection of methyl-lysine binding sites, we solved the 1.8 A structure of the Pc chromodomain in complex with a H3 peptide bearing trimethyl-Lys 27, and compared it with our previously determined structure of the HP1 chromodomain in complex with a H3 peptide bearing trimethyl-Lys 9. The Pc chromodomain distinguishes its methylation target on the H3 tail via an extended recognition groove that binds five additional residues preceding the ARKS motif.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908-0733, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein
A
72Drosophila melanogasterGene Names: Pc
Find proteins for P26017 (Drosophila melanogaster)
Go to UniProtKB:  P26017
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
B
18Drosophila melanogasterGene Names: His3.3A, His3.3B
Find proteins for P84249 (Drosophila melanogaster)
Go to UniProtKB:  P84249
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.120α = 90.00
b = 75.810β = 90.00
c = 80.460γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
CCP4data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance