5AVC: Human Nucleosome Core Particle

Citation:
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 A and 2.2 A 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.
PDB ID: 5AVCDownload
MMDB ID: 135036
PDB Deposition Date: 2015/6/12
Updated in MMDB: 2015/12
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
Similar Structures:
Biological Unit for 5AVC: decameric; determined by author and by software (PISA)
Molecular Components in 5AVC
Label Count Molecule
Proteins (8 molecules)
2
Histone H3.1(Gene symbol: HIST1H3A)
Molecule annotation
2
Histone H4(Gene symbol: HIST1H4I)
Molecule annotation
2
Histone H2A Type 1-b/e(Gene symbol: HIST1H2AE)
Molecule annotation
2
Histone H2B Type 1-J(Gene symbol: HIST1H2BJ)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (147-mer)
Molecule annotation
1
DNA (147-mer)
Molecule annotation
Chemicals (14 molecules)
1
14
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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