6V2K

The nucleosome structure after H2A-H2B exchange

Summary for 6V2K

• Entry DOI: 10.2210/pdb6v2k/pdb
• Descriptor: Histone H3.1, Histone H4, Histone H2A, ... (7 entities in total)
• Functional Keywords: nucleosome, histone exchange, nuclear protein-dna complex, nuclear protein/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 10
• Total formula weight: 202921.88

Authors

Arimura, Y.,Hirano, R.,Kurumizaka, H. (deposition date: 2019-11-24, release date: 2020-11-25, Last modification date: 2023-10-11)

Primary citation

Hirano, R.,Arimura, Y.,Kujirai, T.,Shibata, M.,Okuda, A.,Morishima, K.,Inoue, R.,Sugiyama, M.,Kurumizaka, H.
Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome.
Commun Biol, 4:191-191, 2021

PubMed Abstract: H2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate "open conformation", in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome.

PubMed: 33580188
DOI: 10.1038/s42003-021-01707-z

Experimental method

X-RAY DIFFRACTION (2.6 Å)