3UT9

Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L)

Summary for 3UT9

• Entry DOI: 10.2210/pdb3ut9/pdb
• Descriptor: Histone H3.2, Histone H4, Histone H2A, ... (10 entities in total)
• Functional Keywords: nucleosome core particle, ncp, 601-sequence dna, structural protein-dna complex, structural protein/dna
• Biological source: Xenopus laevis (African clawed frog); More
• Cellular location: Nucleus: P84233 P62799 P02281; Nucleus (By similarity): Q6AZJ8
• Total number of polymer chains: 10
• Total formula weight: 200043.33

Authors

Chua, E.Y.D.,Vasudevan, D.,Davey, G.E.,Wu, B.,Davey, C.A. (deposition date: 2011-11-25, release date: 2012-04-11, Last modification date: 2024-03-20)

Primary citation

Chua, E.Y.D.,Vasudevan, D.,Davey, G.E.,Wu, B.,Davey, C.A.
The mechanics behind DNA sequence-dependent properties of the nucleosome
Nucleic Acids Res., 40:6338-6352, 2012

PubMed 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.

PubMed: 22453276
DOI: 10.1093/nar/gks261

Experimental method

X-RAY DIFFRACTION (2.2 Å)