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PDBsum entry 3lz0
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Structural protein/DNA
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PDB id
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3lz0
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Contents |
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97 a.a.
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83 a.a.
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103 a.a.
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95 a.a.
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78 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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Crystal structures of nucleosome core particles containing the '601' Strong positioning sequence.
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Authors
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D.Vasudevan,
E.Y.Chua,
C.A.Davey.
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Ref.
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J Mol Biol, 2010,
403,
1.
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PubMed id
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Abstract
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Nucleosome positioning plays a key role in genomic regulation by defining
histone-DNA context and by modulating access to specific sites. Moreover, the
histone-DNA register influences the double-helix structure, which in turn can
affect the association of small molecules and protein factors. Analysis of
genomic and synthetic DNA has revealed sequence motifs that direct nucleosome
positioning in vitro; thus, establishing the basis for the DNA sequence
dependence of positioning would shed light on the mechanics of the double helix
and its contribution to chromatin structure in vivo. However, acquisition of
well-diffracting nucleosome core particle (NCP) crystals is extremely dependent
on the DNA fragment used for assembly, and all previous NCP crystal structures
have been based on human α-satellite sequences. Here, we describe the crystal
structures of Xenopus NCPs containing one of the strongest known histone octamer
binding and positioning sequences, the so-called '601' DNA. Two distinct 145-bp
601 crystal forms display the same histone-DNA register, which coincides with
the occurrence of DNA stretching-overtwisting in both halves of the particle
around five double-helical turns from the nucleosome center, giving the DNA an
'effective length' of 147 bp. As we have found previously with stretching around
two turns from the nucleosome center for a centromere-based sequence, the
terminal stretching observed in the 601 constructs is associated with extreme
kinking into the minor groove at purine-purine (pyrimidine-pyrimidine)
dinucleotide steps. In other contexts, these step types display an overall
nonflexible behavior, which raises the possibility that DNA stretching in the
nucleosome or extreme distortions in general have unique sequence dependency
characteristics. Our findings indicate that DNA stretching is an intrinsically
predisposed site-specific property of the nucleosome and suggest how NCP crystal
structures with diverse DNA sequences can be obtained.
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