3LEL

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

Summary for 3LEL

• Entry DOI: 10.2210/pdb3lel/pdb
• Related: 1KX5
• Descriptor: Histone H3.2, Histone H4, Histone H2A, ... (7 entities in total)
• Functional Keywords: nucleosome, nucleosome positioning, dna flexibility, chromatin, acetylation, chromosomal protein, dna-binding, methylation, nucleosome core, nucleus, 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: 20
• Total formula weight: 401116.77

Authors

Wu, B.,Vasudevan, D.,Davey, C.A. (deposition date: 2010-01-15, release date: 2010-05-19, Last modification date: 2023-11-01)

Primary citation

Wu, B.,Mohideen, K.,Vasudevan, D.,Davey, C.A.
Structural insight into the sequence dependence of nucleosome positioning
Structure, 18:528-536, 2010

PubMed Abstract: Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.

PubMed: 20399189
DOI: 10.1016/j.str.2010.01.015

Experimental method

X-RAY DIFFRACTION (2.95 Å)