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PDBsum entry 1kx4
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Structural protein/DNA
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PDB id
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1kx4
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Contents |
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98 a.a.
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83 a.a.
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103 a.a.
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99 a.a.
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78 a.a.
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94 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution.
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Authors
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C.A.Davey,
D.F.Sargent,
K.Luger,
A.W.Maeder,
T.J.Richmond.
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Ref.
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J Mol Biol, 2002,
319,
1097-1113.
[DOI no: ]
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PubMed id
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Abstract
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Solvent binding in the nucleosome core particle containing a 147 base pair,
defined-sequence DNA is characterized from the X-ray crystal structure at 1.9 A
resolution. A single-base-pair increase in DNA length over that used previously
results in substantially improved clarity of the electron density and accuracy
for the histone protein and DNA atomic coordinates. The reduced disorder has
allowed for the first time extensive modeling of water molecules and ions. Over
3000 water molecules and 18 ions have been identified. Water molecules acting as
hydrogen-bond bridges between protein and DNA are approximately equal in number
to the direct hydrogen bonds between these components. Bridging water molecules
have a dual role in promoting histone-DNA association not only by providing
further stability to direct protein-DNA interactions, but also by enabling
formation of many additional interactions between more distantly related
elements. Water molecules residing in the minor groove play an important role in
facilitating insertion of arginine side-chains. Water structure at the interface
of the histones and DNA provides a means of accommodating intrinsic DNA
conformational variation, thus limiting the sequence dependency of nucleosome
positioning while enhancing mobility. Monovalent anions are bound near the N
termini of histone alpha-helices that are not occluded by DNA phosphate groups.
Their location in proximity to the DNA phosphodiester backbone suggests that
they damp the electrostatic interaction between the histone proteins and the
DNA. Divalent cations are bound at specific sites in the nucleosome core
particle and contribute to histone-histone and histone-DNA interparticle
interactions. These interactions may be relevant to nucleosome association in
arrays.
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Figure 2.
Figure 2. Solvation of NCP147. (a) Water molecules and ions
associated with NCP147. The view is as in Figure 1(b). Water
molecules (gold) are shown as spheres of half van der Waals
radius. Manganese ions (violet) and chloride ions (green) are
shown as spheres of van der Waals radius. The path of the
histone chains and DNA strands are shown (H3, blue; H4, green;
H2A, yellow; H2B, red; DNA strands, cyan and brown). The histone
N-terminal tails are not shown in their entirety. (b)
Space-filling representation of the DNA and its primary
hydration layer. Water molecules (gold) with centers closer than
3.5 Å from any DNA atom center are shown. The DNA
superhelix (backbones strands, cyan and brown; bases, silver) is
rotated 60° around the dyad axis compared to the view in
(a). (c) Minor groove "spine of hydration". Five and six-member
fused rings of water molecules (red) with hydrogen bonds
(broken, white) are shown in the DNA minor groove with the
simulated-annealing, omit difference electron density (F[o]
-F[c], 1.3s contour, yellow) superimposed.
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Figure 6.
Figure 6. Specific histone-histone interparticle
interactions in the NCP147 crystals. (a) Two adjacent
side-chains in the histone H4 N-terminal tail, H4-R23 and
H4-L22, and a Mn2+ ion (magenta) participate in extensive
interactions with a highly acidic region of the H2A-H2B dimer of
a neighboring nucleosome core. (b) (stereograph) A Mn2+ ion
(magenta) connects H3-D77 in the H3-H4 tetramer of one particle
with H2B-V45 in the H2A-H2B dimer of an adjacent particle. Both
of these amino acid residues enter the coordination sphere of
the divalent cation. The mean length over all six Mn2+-oxygen
bonds (magenta) is 2.25 Å. Hydrogen bonds made directly
between histone moieties (white) or via water molecules (yellow)
are shown. (c) (stereograph) The guanidinium group of H4-R23, in
a site adjacent to the Mn2+ ion of (b), makes four direct
hydrogen bonds to three surrounding side-chains of the
neighboring H2A-H2B dimer.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2002,
319,
1097-1113)
copyright 2002.
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Secondary reference #1
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Title
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Crystal structure of the nucleosome core particle at 2.8 a resolution.
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Authors
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K.Luger,
A.W.Mäder,
R.K.Richmond,
D.F.Sargent,
T.J.Richmond.
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Ref.
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Nature, 1997,
389,
251-260.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 H3-H4 histone-fold pair. The  1-L1-
2-L2-
3
structural elements are shown. A pseudodyad axis of symmetry
runs vertically through SHL1.5. Side chains that make hydrogen
bonds or hydrophobic interactions with the DNA backbones, and
arginines inserted in the minor groove are shown.
Main-chain-to-DNA-phosphate hydrogen bonds are shown in magenta.
Leucine 65 is in contact with a thymidine methyl group (yellow
bond). Two of three arginine-threonine pairs are hydrogen bonded
(cyan bond). b, H2A-H2B histone-fold pair. As in a, except that
the pseudodyad axis runs through SHL4.5. c, H3-H4 L1L2
DNA-binding site. The H3 L1 and H4 L2 loops make 3 hydrogen
bonds (cyan) with each other in a parallel  -structure.
The L2 loop contains buried hydrogen bonds (cyan) between H4-R78
and H4-D85. The hydrogen-bonding interactions (magenta) between
protein and DNA-phosphate groups involve both main-chain amide
atoms and side-chain atoms. d, H2A-H2B L1L2 DNA-binding site. In
contrast to the H3 L1 and H4 L2 loops, the other three L1L2
sites have only one well formed -structure
hydrogen bond, as for H2A L1 and H2B L2 shown here (cyan). An
arginine (H2B-R83) hydrogen bonds to a phosphate group instead
of an acidic side chain (H2B-E90), as occurs at the homologous
sites in the other L1L2 loops. e, H3'-H3 4-helix bundle. The
H3-H4 histone pairs form the tetramer through the interaction of
the C-terminal halves of the 2
helices and the 3
helix of H3' and H3 across the molecular dyad axis. Histidine
113' makes a buried hydrogen bond to link the H3 molecules. In
addition, several hydrophobic interactions occur. f, H2B-H4
4-helix bundle. The H2A-H2B dimer assembles into the histone
octamer through the interaction of H2B with H4. The hydrogen
bond of H4-H75 to H2B-E90 is analogous to that in H3'-H3, but is
not buried here because of the orientation of H2B-R83. Across
the pseudo-twofold axis, however, H2B-Y80 replaces the H4
histidine and, together with H4-Y72 and H4-Y88, forms a
hydrophobic cluster.
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Figure 3.
Figure 3 Histone tails between DNA gyres. The H2B (red) and
H3 (blue) N-terminal tails pass through channels in the DNA
superhelix (white) formed by aligned minor grooves. b, H3 tail
segment in minor-groove channel. The H3 tail sequence HRYRP
passes through the juxtaposed minor grooves of SHL -7 (DNA
terminus) and SHL1 (DNA centre). The electron density (magenta)
clearly identifies the conformation of these amino acids. c, H4
tail bound to the H2A-H2B dimer. The electrostatic surface of
the nucleosome core particle shows an intensely negatively
charged region (bright red) near the centre of its exposed
protein face. Amino acids 16-25 of the H4 tail lie on this
region of the H2A-H2B dimer, which contains 7 clustered acidic
side chains. The orientation of the particle is as for Fig. 1d .
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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