1GUW

STRUCTURE OF THE CHROMODOMAIN FROM MOUSE HP1beta IN COMPLEX WITH THE LYSINE 9-METHYL HISTONE H3 N-TERMINAL PEPTIDE, NMR, 25 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 25 
  • Selection Criteria: LOWEST ENERGY OF 75 CONVERGED STRUCTURES 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Hp1 Chromodomain Bound to Histone H3 Methylated at Lysine 9

Nielsen, P.R.Nietlispach, D.Mott, H.R.Callaghan, J.M.Bannister, A.Kouzarides, T.Murzin, A.G.Murzina, N.V.Laue, E.D.

(2002) Nature 416: 103-107

  • DOI: 10.1038/nature722

  • PubMed Abstract: 
  • Specific modifications to histones are essential epigenetic markers---heritable changes in gene expression that do not affect the DNA sequence. Methylation of lysine 9 in histone H3 is recognized by heterochromatin protein 1 (HP1), which directs the ...

    Specific modifications to histones are essential epigenetic markers---heritable changes in gene expression that do not affect the DNA sequence. Methylation of lysine 9 in histone H3 is recognized by heterochromatin protein 1 (HP1), which directs the binding of other proteins to control chromatin structure and gene expression. Here we show that HP1 uses an induced-fit mechanism for recognition of this modification, as revealed by the structure of its chromodomain bound to a histone H3 peptide dimethylated at Nzeta of lysine 9. The binding pocket for the N-methyl groups is provided by three aromatic side chains, Tyr21, Trp42 and Phe45, which reside in two regions that become ordered on binding of the peptide. The side chain of Lys9 is almost fully extended and surrounded by residues that are conserved in many other chromodomains. The QTAR peptide sequence preceding Lys9 makes most of the additional interactions with the chromodomain, with HP1 residues Val23, Leu40, Trp42, Leu58 and Cys60 appearing to be a major determinant of specificity by binding the key buried Ala7. These findings predict which other chromodomains will bind methylated proteins and suggest a motif that they recognize.


    Related Citations: 
    • Structure of the Chromatin Binding (Chromo) Domain from Mouse Modifier Protein 1
      Ball, L.J.,Murzina, N.V.,Broadhurst, R.W.,Raine, A.R.,Archer, S.J.,Stott, F.J.,Murzin, A.G.,Singh, P.B.,Domaille, P.J.,Laue, E.D.
      (1997) Embo J. 16: 2437


    Organizational Affiliation

    Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHROMOBOX PROTEIN HOMOLOG 1
A
73Mus musculusGene Names: Cbx1 (Cbx)
Find proteins for P83917 (Mus musculus)
Go to UniProtKB:  P83917
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3.1
B
18Mus musculusGene Names: Hist1h3a, Hist1h3g, Hist1h3h, Hist1h3i (H3a, H3.1-221, H3g, H3.1-291, H3h, H3.1-I, H3i)
Find proteins for P68433 (Mus musculus)
Go to UniProtKB:  P68433
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 25 
  • Selection Criteria: LOWEST ENERGY OF 75 CONVERGED STRUCTURES 
  • Olderado: 1GUW Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Database references