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PDBsum entry 3c1c
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Structural protein/DNA
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PDB id
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3c1c
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Contents |
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98 a.a.
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78 a.a.
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105 a.a.
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93 a.a.
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84 a.a.
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References listed in PDB file
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Key reference
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Title
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The effect of h3k79 dimethylation and h4k20 trimethylation on nucleosome and chromatin structure.
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Authors
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X.Lu,
M.D.Simon,
J.V.Chodaparambil,
J.C.Hansen,
K.M.Shokat,
K.Luger.
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Ref.
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Nat Struct Biol, 2008,
15,
1122-1124.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 1.
(a) Location of H3K79 and H4K20 (red) on the unmodified NCP
structure (surface representation; PDB 1AOI). Histones H2A, H2B,
H3 and H4 are shown in light yellow, red, blue and green,
respectively. (b) H3K[c]79me2 adopts an alternative side chain
conformation. The structures of the NCP containing H3[c]79me2
(light blue and light green) were superimposed onto unmodified
NCP (dark blue and dark green). H3K[c]79me2 is shown in yellow
and unmodified K79 is shown in red. (c) Electrostatic potential
of the same region in NCP containing H3K[c]79me2 as shown in b.
(d) The equivalent region for unmodified NCP. Red indicates
negative surface potential and blue indicates positive surface
potential, scaled from -15 to +15. Note the small hydrophobic
cavity (indicated with an arrow in c) that is uncovered by the
reorientation of H3K[c]79me2. (e) Superposition of nucleosomes
with H4K[c]20me3 (light green, light blue) with unmodified NCP
(dark green, dark blue). (f) Superposition of H4 tails from
published nucleosome structures. Blue, human NCP (PDB 2CV5)^19;
yellow, X. laevis NCP (PDB 1KX5)^20; red, acetylated histone H4
(PDB 16EI)^21; green, NCP with H4K[c]20me3 (this work, PDB 3C1B).
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Figure 2.
(a–c) Analysis was carried out in TEN buffer (a), in buffer
contain 1 mM MgCl[2] (b) and 1.5 mM MgCl[2] (c). (d)
Self-association of unmodified, H3K[c]79me2 and H4K[c]20Me3
nucleosomal arrays. Symbols in a–d:  circle
, H3K[c]79me2 nucleosomal array;  ,
unmodified nucleosomal array;  triangle
, H4K[c]20Me3 nucleosomal array. The experiments were repeated
three times with identical results (see also Supplementary Fig.
3); one representative experiment is shown. Error bars are s.d.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
Nat Struct Biol
(2008,
15,
1122-1124)
copyright 2008.
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