3C1B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 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:  
    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 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3-likeAE135Xenopus laevisMutation(s): 0 
Gene Names: Histone H3
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF102Xenopus laevisMutation(s): 0 
Gene Names: Histone H4
Find proteins for P62799 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1CG129Xenopus laevisMutation(s): 0 
Gene Names: Histone H2A
Find proteins for P06897 (Xenopus laevis)
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Go to UniProtKB:  P06897
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone 2, H2bfDH125Xenopus tropicalisMutation(s): 0 
Gene Names: hist2h2bfTGas058p09.1-001LOC108648864LOC108648866XENTR_v90029327mgXENTR_v90029353mg
Find proteins for Q28D68 (Xenopus tropicalis)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Palindromic 146bp Human Alpha satellite DNAI, J146N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ML3
Query on ML3
B,FL-PEPTIDE LINKINGC8 H19 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.67α = 90
b = 109.83β = 90
c = 181.03γ = 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 

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