9JC6 image
Deposition Date 2024-08-28
Release Date 2025-09-03
Last Version Date 2025-09-24
Entry Detail
PDB ID:
9JC6
Title:
Human H2BW2 nucleosome
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.34 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.1
Gene (Uniprot):H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
Chain IDs:A, E
Chain Length:135
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:B, F
Chain Length:102
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:C, G
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Isoform 2 of Histone H2B type F-M
Gene (Uniprot):H2BW2
Chain IDs:D, H
Chain Length:147
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:147-mer DNA
Chain IDs:I
Chain Length:147
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:147-mer DNA
Chain IDs:J
Chain Length:147
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
H2B.W2, a spermatocyte-specific histone variant, disrupts nucleosome stability, and reduces chromatin compaction.
Nucleic Acids Res. 53 ? ? (2025)
PMID: 40874595 DOI: 10.1093/nar/gkaf825

Abstact

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.

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Disease

Primary Citation of related structures