9JC6

Human H2BW2 nucleosome

Summary for 9JC6

• Entry DOI: 10.2210/pdb9jc6/pdb
• EMDB information: 61358
• Descriptor: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total)
• Functional Keywords: nucleosome, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 204747.08

Authors

Ding, D.B.,Ishibashi, T.,Nguyen, T.T. (deposition date: 2024-08-28, release date: 2025-09-03, Last modification date: 2025-09-24)

Primary citation

Nguyen, A.T.T.,Ding, D.,Bai, X.,Pang, M.Y.H.,Deng, M.,Liu, Y.,Jin, T.,Xu, Z.,Zhang, Y.,Zhai, Y.,Yan, Y.,Ishibashi, T.
H2B.W2, a spermatocyte-specific histone variant, disrupts nucleosome stability, and reduces chromatin compaction.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Spermatogenesis is a highly regulated process that requires precise chromatin remodeling, which includes the incorporation of testis-specific histone variants. While several of these variants have been characterized, the role of H2B.W2, a member of the H2BW family, remains largely unclear. Here, we showed that H2B.W2 expression occurs mainly in spermatocytes, slightly later than its paralog H2B.W1. Cryo-electron microscopy analysis of H2B.W2-containing nucleosomes reveals a more relaxed conformation compared to canonical nucleosomes caused by weakened interactions between the outer DNA turn and the histone core. We pinpointed the N-terminal tail and α2 helix of H2B.W2 as critical regions for nucleosome destabilization. Furthermore, we identify G73 within the L1 loop as a key residue involved in disrupting higher-order chromatin structure. Our findings suggest that H2B.W2-mediated nucleosome and chromatin destabilization may play a role in regulating gene expression during spermatogenesis, with potential implications for sperm development and function.

PubMed: 40874595
DOI: 10.1093/nar/gkaf825

Experimental method

ELECTRON MICROSCOPY (3.34 Å)