3KXB

Structural characterization of H3K56Q nucleosomes and nucleosomal arrays


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural characterization of H3K56Q nucleosomes and nucleosomal arrays.

Watanabe, S.Resch, M.Lilyestrom, W.Clark, N.Hansen, J.C.Peterson, C.Luger, K.

(2010) Biochim.Biophys.Acta 1799: 480-486

  • DOI: 10.1016/j.bbagrm.2010.01.009
  • Primary Citation of Related Structures:  3KWQ

  • PubMed Abstract: 
  • The post-translational modification of histones is a key mechanism for the modulation of DNA accessibility. Acetylated lysine 56 in histone H3 is associated with nucleosome assembly during replication and DNA repair, and is thus likely to predominate ...

    The post-translational modification of histones is a key mechanism for the modulation of DNA accessibility. Acetylated lysine 56 in histone H3 is associated with nucleosome assembly during replication and DNA repair, and is thus likely to predominate in regions of chromatin containing nucleosome-free regions. Here we show by X-ray crystallography that mutation of H3 lysine 56 to glutamine (to mimic acetylation) or glutamate (to cause a charge reversal) has no detectable effects on the structure of the nucleosome. At the level of higher order chromatin structure, the K to Q substitution has no effect on the folding of model nucleosomal arrays in cis, regardless of the degree of nucleosome density. In contrast, defects in array-array interactions in trans ('oligomerization') are selectively observed for mutant H3 lysine 56 arrays that contain nucleosome-free regions. Our data suggests that H3K56 acetylation is one of the molecular mechanisms employed to keep chromatin with nucleosome-free regions accessible to the DNA replication and repair machinery.


    Organizational Affiliation

    Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St., Worcester, MA 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
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
C, G
129Xenopus laevisGene Names: hist1h2aj (LOC494591)
Find proteins for Q6AZJ8 (Xenopus laevis)
Go to UniProtKB:  Q6AZJ8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
122Xenopus laevisN/A
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 5
MoleculeChainsLengthOrganism
PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNAI,J146N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.283 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.517α = 90.00
b = 105.670β = 90.00
c = 181.330γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance