3G7L

Chromodomain of Chp1 in complex with Histone H3K9me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin

Schalch, T.Job, G.Noffsinger, V.J.Shanker, S.Kuscu, C.Joshua-Tor, L.Partridge, J.F.

(2009) Mol.Cell 34: 36-46

  • DOI: 10.1016/j.molcel.2009.02.024

  • PubMed Abstract: 
  • In fission yeast, assembly of centromeric heterochromatin requires the RITS complex, which consists of Ago1, Tas3, Chp1, and siRNAs derived from centromeric repeats. Recruitment of RITS to centromeres has been proposed to depend on siRNA-dependent ta ...

    In fission yeast, assembly of centromeric heterochromatin requires the RITS complex, which consists of Ago1, Tas3, Chp1, and siRNAs derived from centromeric repeats. Recruitment of RITS to centromeres has been proposed to depend on siRNA-dependent targeting of Ago1 to centromeric sequences. Previously, we demonstrated that methylated lysine 9 of histone H3 (H3K9me) acts upstream of siRNAs during heterochromatin establishment. Our crystal structure of Chp1's chromodomain in complex with a trimethylated lysine 9 H3 peptide reveals extensive sites of contact that contribute to Chp1's high-affinity binding. We found that this high-affinity binding is critical for the efficient establishment of centromeric heterochromatin, but preassembled heterochromatin can be maintained when Chp1's affinity for H3K9me is greatly reduced.


    Organizational Affiliation

    Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chromo domain-containing protein 1
A
61Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: chp1
Find proteins for Q10103 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10103
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1/H3.2
P
16Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 1 
Gene Names: hht1, hht2
Find proteins for P09988 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P09988
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
P
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 41.560α = 90.00
b = 41.560β = 90.00
c = 87.380γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance