3C1B

The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure.

Lu, X.Simon, M.D.Chodaparambil, J.V.Hansen, J.C.Shokat, K.M.Luger, K.

(2008) Nat.Struct.Mol.Biol. 15: 1122-1124

  • DOI: 10.1038/nsmb.1489
  • Primary Citation of Related Structures:  3C1C

  • PubMed Abstract: 
  • Histone methylation regulates chromatin function dependent on the site and degree of the modification. In addition to creating binding sites for proteins, methylated lysine residues are likely to influence chromatin structure directly. Here we presen ...

    Histone methylation regulates chromatin function dependent on the site and degree of the modification. In addition to creating binding sites for proteins, methylated lysine residues are likely to influence chromatin structure directly. Here we present crystal structures of nucleosomes reconstituted with methylated histones and investigate the folding behavior of resulting arrays. We demonstrate that dimethylation of histone H3 at lysine residue 79 locally alters the nucleosomal surface, whereas trimethylation of H4 at lysine residue 20 affects higher-order structure.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, 1385 Center Avenue, Fort Collins, Colorado 80523-1870, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3-like
A, E
135Xenopus laevisN/A
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisN/A
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
129Xenopus laevisN/A
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone 2, H2bf
D, H
125Xenopus tropicalisGene Names: hist2h2bf (LOC100487281)
Find proteins for Q28D68 (Xenopus tropicalis)
Go to UniProtKB:  Q28D68
Entity ID: 5
MoleculeChainsLengthOrganism
Palindromic 146bp Human Alpha satellite DNAI,J146N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ML3
Query on ML3
B, F
L-peptide linkingC8 H19 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.670α = 90.00
b = 109.830β = 90.00
c = 181.030γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance