5AVC

human nucleosome core particle

Summary for 5AVC

• Entry DOI: 10.2210/pdb5avc/pdb
• Related: 5av5 5av6 5av8 5av9 5avb
• Descriptor: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (8 entities in total)
• Functional Keywords: nucleosome core particle, ncp, acetylation, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 10
• Total formula weight: 203168.75

Authors

Wakamori, M.,Fujii, Y.,Umehara, T.,Yokoyama, S. (deposition date: 2015-06-12, release date: 2015-12-23, Last modification date: 2024-03-20)

Primary citation

Wakamori, M.,Fujii, Y.,Suka, N.,Shirouzu, M.,Sakamoto, K.,Umehara, T.,Yokoyama, S.
Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation
Sci Rep, 5:17204-17204, 2015

PubMed Abstract: Post-translational modifications (PTMs) of histones, such as lysine acetylation of the N-terminal tails, play crucial roles in controlling gene expression. Due to the difficulty in reconstituting site-specifically acetylated nucleosomes with crystallization quality, structural analyses of histone acetylation are currently performed using synthesized tail peptides. Through engineering of the genetic code, translation termination, and cell-free protein synthesis, we reconstituted human H4-mono- to tetra-acetylated nucleosome core particles (NCPs), and solved the crystal structures of the H4-K5/K8/K12/K16-tetra-acetylated NCP and unmodified NCP at 2.4 Å and 2.2 Å resolutions, respectively. The structure of the H4-tetra-acetylated NCP resembled that of the unmodified NCP, and the DNA wrapped the histone octamer as precisely as in the unmodified NCP. However, the B-factors were significantly increased for the peripheral DNAs near the N-terminal tail of the intra- or inter-nucleosomal H4. In contrast, the B-factors were negligibly affected by the H4 tetra-acetylation in histone core residues, including those composing the acidic patch, and at H4-R23, which interacts with the acidic patch of the neighboring NCP. The present study revealed that the H4 tetra-acetylation impairs NCP self-association by changing the interactions of the H4 tail with DNA, and is the first demonstration of crystallization quality NCPs reconstituted with genuine PTMs.

PubMed: 26607036
DOI: 10.1038/srep17204

Experimental method

X-RAY DIFFRACTION (2.4 Å)