9R1D

Structure of the H3.V-H4.V variant nucleosome core particle from Trypanosoma brucei

Summary for 9R1D

• Entry DOI: 10.2210/pdb9r1d/pdb
• EMDB information: 53505
• Descriptor: Histone H3 variant, Histone H4, Histone H2A, ... (6 entities in total)
• Functional Keywords: nucleosome, histone, nucleus, dna binding protein
• Biological source: Trypanosoma brucei brucei TREU927; More
• Total number of polymer chains: 10
• Total formula weight: 196799.58

Authors

Deak, G.,Wilson, M.D. (deposition date: 2025-04-26, release date: 2026-01-28, Last modification date: 2026-03-04)

Primary citation

Deak, G.,Burdett, H.,Watson, J.A.,Wilson, M.D.
Trypanosome histone variants H3.V and H4.V promote nucleosome plasticity in repressed chromatin.
Structure, 2026

PubMed Abstract: Histone variants define distinct chromatin states by modulating the biophysical properties of nucleosomes. Variants play a particularly important role in the parasitic protist Trypanosoma brucei, which has unusual chromatin and lacks a canonical repressive heterochromatin system. Instead, T. brucei utilizes specialized divergent histone variants H3.V and H4.V. However, the biochemical basis of their repressive functions is unknown. Here, we determined the structure of the H3.V-H4.V nucleosome core particle and biochemically characterized variant-containing nucleosomes and nucleosome arrays, probing their unique properties. We discovered that surprisingly for repressive-state nucleosomes, H3.V promotes pronounced DNA splaying, largely via its N-terminal tail region, while retaining overall stability that is comparable to canonical nucleosomes. In contrast, H4.V exhibits near-identical binding to DNA but mediates a slight increase in histone octamer stability. The surface of the H3.V-H4.V nucleosome is altered and provides a differential platform for chromatin-binding proteins, linking the variants to parasite pathogenicity.

PubMed: 41709455
DOI: 10.1016/j.str.2026.01.008

Experimental method

ELECTRON MICROSCOPY (3.21 Å)