6ESG

Nucleosome breathing : Class 2

Summary for 6ESG

• Entry DOI: 10.2210/pdb6esg/pdb
• EMDB information: 3948
• Descriptor: Histone H3.2, Histone H4, Histone H2A, ... (6 entities in total)
• Functional Keywords: nucleosome, nucleosome breathing, hexasome, gene regulation
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 10
• Total formula weight: 198890.11

Authors

Bilokapic, S.,Halic, M. (deposition date: 2017-10-20, release date: 2017-12-20, Last modification date: 2024-05-15)

Primary citation

Bilokapic, S.,Strauss, M.,Halic, M.
Histone octamer rearranges to adapt to DNA unwrapping.
Nat. Struct. Mol. Biol., 25:101-108, 2018

PubMed Abstract: Nucleosomes, the basic units of chromatin, package and regulate expression of eukaryotic genomes. Although the structure of the intact nucleosome is well characterized, little is known about structures of partially unwrapped, transient intermediates. In this study, we present nine cryo-EM structures of distinct conformations of nucleosome and subnucleosome particles. These structures show that initial DNA breathing induces conformational changes in the histone octamer, particularly in histone H3, that propagate through the nucleosome and prevent symmetrical DNA opening. Rearrangements in the H2A-H2B dimer strengthen interaction with the unwrapping DNA and promote nucleosome stability. In agreement with this, cross-linked H2A-H2B that cannot accommodate unwrapping of the DNA is not stably maintained in the nucleosome. H2A-H2B release and DNA unwrapping occur simultaneously, indicating that DNA is essential in stabilizing the dimer in the nucleosome. Our structures reveal intrinsic nucleosomal plasticity that is required for nucleosome stability and might be exploited by extrinsic protein factors.

PubMed: 29323273
DOI: 10.1038/s41594-017-0005-5

Experimental method

ELECTRON MICROSCOPY (5.4 Å)