8JBX

Human canonical 601 DNA nucleosome

Summary for 8JBX

• Entry DOI: 10.2210/pdb8jbx/pdb
• EMDB information: 36148
• Descriptor: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total)
• Functional Keywords: histone, 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: 199567.96

Authors

Ding, D.B.,Ishibashi, T.,Nguyen, T.T. (deposition date: 2023-05-09, release date: 2024-05-15, Last modification date: 2024-11-06)

Primary citation

Ding, D.,Pang, M.Y.H.,Deng, M.,Nguyen, T.T.,Liu, Y.,Sun, X.,Xu, Z.,Zhang, Y.,Zhai, Y.,Yan, Y.,Ishibashi, T.
Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA-histone interactions.
Nucleic Acids Res., 2024

PubMed Abstract: Multiple testis-specific histone variants are involved in the dynamic chromatin transitions during spermatogenesis. H2B.W1 (previously called H2BFWT) is an H2B variant specific to primate testis with hitherto unclear functions, although its single-nucleotide polymorphisms (SNPs) are closely associated with male non-obstructive infertility. Here, we found that H2B.W1 is only expressed in the mid-late spermatogonia stages, and H2B.W1 nucleosomes are defined by a more flexible structure originating from weakened interactions between histones and DNA. Furthermore, one of its SNPs, H2B.W1-H100R, which is associated with infertility, further destabilizes the nucleosomes and increases the nucleosome unwrapping rate by interfering with the R100 and H4 K91/R92 interaction. Our results suggest that destabilizing H2B.W1 containing nucleosomes might change the chromatin structure of spermatogonia, and that H2B.W1-H100R enhances the nucleosome-destabilizing effects, leading to infertility.

PubMed: 39329259
DOI: 10.1093/nar/gkae825

Experimental method

ELECTRON MICROSCOPY (3.35 Å)