9B3P

The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome

Summary for 9B3P

• Entry DOI: 10.2210/pdb9b3p/pdb
• EMDB information: 44148
• Descriptor: Histone H3.3, Histone H4, Histone H2A.Z, ... (6 entities in total)
• Functional Keywords: histone variant, nucleosome, chromatin, complex, structural protein, structural protein-dna complex, structural protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 205478.64

Authors

Tan, D.,Sokolova, V. (deposition date: 2024-03-19, release date: 2024-06-12, Last modification date: 2024-07-17)

Primary citation

Jung, H.,Sokolova, V.,Lee, G.,Stevens, V.R.,Tan, D.
Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z.
Epigenomes, 8:-, 2024

PubMed Abstract: Variant H3.3, along with H2A.Z, is notably enriched at promoter regions and is commonly associated with transcriptional activation. However, the specific molecular mechanisms through which H3.3 influences chromatin dynamics at transcription start sites, and its role in gene regulation, remain elusive. Using a combination of biochemistry and cryo-electron microscopy (cryo-EM), we show that the inclusion of H3.3 alone does not induce discernible changes in nucleosome DNA dynamics. Conversely, the presence of both H3.3 and H2A.Z enhances DNA's flexibility similarly to H2A.Z alone. Interestingly, our findings suggest that the presence of H3.3 in the H2A.Z nucleosome provides slightly increased protection to DNA at internal sites within the nucleosome. These results imply that while H2A.Z at active promoters promotes the formation of more accessible nucleosomes with increased DNA accessibility to facilitate transcription, the simultaneous presence of H3.3 offers an additional mechanism to fine-tune nucleosome accessibility and the chromatin environment.

PubMed: 38920622
DOI: 10.3390/epigenomes8020021

Experimental method

ELECTRON MICROSCOPY (3 Å)