3KXB

Structural characterization of H3K56Q nucleosomes and nucleosomal arrays


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.378 

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This is version 1.3 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: https://doi.org/10.1016/j.bbagrm.2010.01.009
  • Primary Citation of Related Structures:  
    3KWQ, 3KXB

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: LOC494591
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
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UniProt GroupQ6AZJ8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 5
MoleculeChains LengthOrganismImage
PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA
I, J
146N/A
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.283 
  • R-Value Observed: 0.378 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.517α = 90
b = 105.67β = 90
c = 181.33γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description