3C1C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/nsmb.1489
  • Primary Citation of Related Structures:  
    3C1B, 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3-like
A, E
135Xenopus laevisMutation(s): 0 
Gene Names: Histone H3
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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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Gene Names: Histone H4
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: Histone H2A
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone 2, H2bf
D, H
125Xenopus tropicalisMutation(s): 0 
Gene Names: hist2h2bfTGas058p09.1-001
UniProt
Find proteins for Q28D68 (Xenopus tropicalis)
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UniProt GroupQ28D68
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Entity ID: 5
MoleculeChains LengthOrganismImage
Palindromic 146bp Human Alpha satellite DNA
I, J
146N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M2L
Query on M2L
A, E
L-PEPTIDE LINKINGC7 H16 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.03α = 90
b = 110.08β = 90
c = 182.6γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection