1KNE

Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail.

Jacobs, S.A.Khorasanizadeh, S.

(2002) Science 295: 2080-2083

  • DOI: 10.1126/science.1069473
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The chromodomain of the HP1 family of proteins recognizes histone tails with specifically methylated lysines. Here, we present structural, energetic, and mutational analyses of the complex between the Drosophila HP1 chromodomain and the histone H3 ta ...

    The chromodomain of the HP1 family of proteins recognizes histone tails with specifically methylated lysines. Here, we present structural, energetic, and mutational analyses of the complex between the Drosophila HP1 chromodomain and the histone H3 tail with a methyllysine at residue 9, a modification associated with epigenetic silencing. The histone tail inserts as a beta strand, completing the beta-sandwich architecture of the chromodomain. The methylammonium group is caged by three aromatic side chains, whereas adjacent residues form discerning contacts with one face of the chromodomain. Comparison of dimethyl- and trimethyllysine-containing complexes suggests a role for cation-pi and van der Waals interactions, with trimethylation slightly improving the binding affinity.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HETEROCHROMATIN PROTEIN 1
A
69Drosophila melanogasterMutation(s): 4 
Gene Names: Su(var)205 (HP1)
Find proteins for P05205 (Drosophila melanogaster)
Go to UniProtKB:  P05205
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trimethylated Histone H3
P
16Drosophila melanogasterMutation(s): 1 
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
Small Molecules
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: 2.4 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.246 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 33.745α = 90.00
b = 76.943β = 90.00
c = 75.947γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4data scaling
CNSphasing
TRUNCATEdata reduction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance