3KWQ

Structural characterization of H3K56Q nucleosomes and nucleosomal arrays


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.368 

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.

(null) Biochim Biophys Acta 1799: 480-486

  • DOI: 10.1016/j.bbagrm.2010.01.009
  • Structures With Same Primary Citation

  • 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
98Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
83Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
107Xenopus laevisMutation(s): 0 
Gene Names: LOC494591
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
93Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsLengthOrganism
DNA (146-MER)I, J146N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.368 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.561α = 90
b = 109.542β = 90
c = 180.65γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance