5X7X

The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution

Summary for 5X7X

• Entry DOI: 10.2210/pdb5x7x/pdb
• Descriptor: Histone H3.3, Histone H4, Histone H2A type 1-B/E, ... (8 entities in total)
• Functional Keywords: chromatin, nucleosome, histone variant, structural protein-dna complex, structural protein/dna
• Biological source: Homo sapiens (Human); More
• Cellular location: Nucleus: P84243 P62805 P04908 P06899
• Total number of polymer chains: 10
• Total formula weight: 202934.33

Authors

Arimura, Y.,Taguchi, H.,Kurumizaka, H. (deposition date: 2017-02-27, release date: 2017-04-19, Last modification date: 2023-11-22)

Primary citation

Taguchi, H.,Xie, Y.,Horikoshi, N.,Maehara, K.,Harada, A.,Nogami, J.,Sato, K.,Arimura, Y.,Osakabe, A.,Kujirai, T.,Iwasaki, T.,Semba, Y.,Tachibana, T.,Kimura, H.,Ohkawa, Y.,Kurumizaka, H.
Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8
Biochemistry, 56:2184-2196, 2017

PubMed Abstract: Non-allelic histone variants are considered as epigenetic factors that regulate genomic DNA functions in eukaryotic chromosomes. In this study, we identified three new human histone H3 variants (named H3.6, H3.7, and H3.8), which were previously annotated as pseudogenes. H3.6 and H3.8 conserve the H3.3-specific amino acid residues, but H3.7 shares the specific amino acid residues with H3.1. We successfully reconstituted the nucleosome containing H3.6 in vitro and determined its crystal structure. In the H3.6 nucleosome, the H3.6-specific Val62 residue hydrophobically contacts the cognate H4 molecule, but its contact area is smaller than that of the corresponding H3.3 Ile62 residue. The thermal stability assay revealed that the H3.6 nucleosome is substantially unstable, as compared to the H3.3 nucleosome. Interestingly, mutational analysis demonstrated that the H3.6 Val62 residue is fully responsible for the H3.6 nucleosome instability, probably because of the weakened hydrophobic interaction with H4. We also reconstituted the nucleosome containing H3.8, but its thermal stability was quite low. In contrast, purified H3.7 failed to form nucleosomes in vitro. The identification and characterization of these novel human histone H3 variants provide important new insights into understanding the epigenetic regulation of the human genome.

PubMed: 28374988
DOI: 10.1021/acs.biochem.6b01098

Experimental method

X-RAY DIFFRACTION (2.184 Å)