3UTA: Crystal Structure Of Nucleosome Core Particle Assembled With An Alpha- Satellite Sequence Containing Two Ttaaa Elements (ncp-ta2)

Citation:
Abstract
Chromatin organization and composition impart sophisticated regulatory features critical to eukaryotic genomic function. Although DNA sequence-dependent histone octamer binding is important for nucleosome activity, many aspects of this phenomenon have remained elusive. We studied nucleosome structure and stability with diverse DNA sequences, including Widom 601 derivatives with the highest known octamer affinities, to establish a simple model behind the mechanics of sequence dependency. This uncovers the unique but unexpected role of TA dinucleotides and a propensity for G|C-rich sequence elements to conform energetically favourably at most locations around the histone octamer, which rationalizes G|C% as the most predictive factor for nucleosome occupancy in vivo. In addition, our findings reveal dominant constraints on double helix conformation by H3-H4 relative to H2A-H2B binding and DNA sequence context-dependency underlying nucleosome structure, positioning and stability. This provides a basis for improved prediction of nucleosomal properties and the design of tailored DNA constructs for chromatin investigations.
PDB ID: 3UTADownload
MMDB ID: 98691
PDB Deposition Date: 2011/11/25
Updated in MMDB: 2013/06
Experimental Method:
x-ray diffraction
Resolution: 2.07  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 3UTA: decameric; determined by author and by software (PISA)
Molecular Components in 3UTA
Label Count Molecule
Proteins (8 molecules)
2
Histone H3.2(Gene symbol: hist2h3c.L)
Molecule annotation
2
Histone H4(Gene symbol: hist1h4a.L)
Molecule annotation
2
Histone H2A
Molecule annotation
2
Histone H2B 1.1(Gene symbol: hist1h2bj.S)
Molecule annotation
Nucleotides(2 molecules)
1
145-mer DNA
Molecule annotation
1
145-mer DNA
Molecule annotation
Chemicals (21 molecules)
1
4
2
17
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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