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PDBsum entry 1m1a
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Structural protein/DNA
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PDB id
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1m1a
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Contents |
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99 a.a.
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80 a.a.
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105 a.a.
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93 a.a.
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93 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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Crystal structures of nucleosome core particles in complex with minor groove DNA-Binding ligands.
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Authors
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R.K.Suto,
R.S.Edayathumangalam,
C.L.White,
C.Melander,
J.M.Gottesfeld,
P.B.Dervan,
K.Luger.
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Ref.
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J Mol Biol, 2003,
326,
371-380.
[DOI no: ]
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PubMed id
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Abstract
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We determined the crystal structures of three nucleosome core particles in
complex with site-specific DNA-binding ligands, the pyrrole-imidazole
polyamides. While the structure of the histone octamer and its interaction with
the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes
significant structural changes at the ligand-binding sites and in adjacent
regions to accommodate the ligands. Our findings suggest that twist diffusion
occurs over long distances through tightly bound nucleosomal DNA. This may be
relevant to the mechanism of ATP-dependent and spontaneous nucleosome
translocation, and to the effect of bound factors on nucleosome dynamics.
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Figure 2.
Figure 2. DNA parameters. (a) Minor groove widths
were averaged for the 10 -- 11 base-pairs between indi-
vidual protein -- DNA contact points, and are plotted
against the superhelix location. Values for X-NCP,
NCP-PA1, NCP-PA2, and NCP-PA3 are plotted against
SHLs in black, blue, green, and magenta, respectively.
The location of polyamides in each structure is indicated
by blue, green, and magenta boxes, respectively. Data
points for SHLs at which stretching occurs are circled;
the equivalent regions in the long half are indicated by
broken-line circles. (b) DNA twist angles, averaged as
in (a). The position of stretch sites is indicated as in (a).
A vertical line indicates the location of the dyad axis
(SHL 0).
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Figure 4.
Figure 4. Stretching of nucleosomal DNA. (a) A schematic describing the alignment procedure. Long (turquoise) and
short DNA halves (black and brown, respectively for NCP-PA1,2 and X-NCP) were aligned using LSQMAN (Uppsala
Software Factory). Base-pair 73 is indicated by F. Stretching of the short half occurs at SHL-5 in NCP-PA1 and 2, and at
SHL-2 in X-NCP. Hatched regions indicate those regions of the short half where the sequence is out of register by one
base-pair compared to the long half. (b) Overview of parts of the structure of NCP-PA1, viewed down the superhelical
axis as in Figure 1(a). Only base-pairs 13 -- 78 (short half) and associated proteins are shown. The long half (turquoise,
base-pairs 68 -- 134) was superimposed onto the short half (white) as described for (a). Polyamide 1 is shown in blue;
histone coloring is as described for Figure 1. The dyad axis is indicated by a broken line, base-pair 73 is indicated by
F, the L1L2 DNA-binding motif is indicated by O, the a1 -- a1 motif is indicated by *. (c) X-NCP with aligned long
and short halves (turquoise and gold, respectively) was superimposed onto NCP-PA1 by a structural alignment of 30
base-pairs centered on either stretching site, as shown in (a). All other labels are as in (b).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
326,
371-380)
copyright 2003.
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