8Q16
CryoEM structure of rice nucleosome containing a H4 variant chimera
This is a non-PDB format compatible entry.
Summary for 8Q16
| Entry DOI | 10.2210/pdb8q16/pdb |
| Related | 8Q15 |
| EMDB information | 18060 18061 |
| Descriptor | Histone H2A.2, Histone H2B.4, Histone H3.2, ... (6 entities in total) |
| Functional Keywords | histone, nucleosome core particle, rice nucleosome, chromatin, dna binding protein |
| Biological source | Oryza More |
| Total number of polymer chains | 10 |
| Total formula weight | 205512.26 |
| Authors | Sotelo-Parrilla, P.,Hari Sundar G, V.,Raju, S.,Jha, S.,Gireesh, A.,Gut, F.,Vinothkumar, K.R.,Berger, F.,Shivaprasad, P.V.,Jeyaprakash, A.A. (deposition date: 2023-07-30, release date: 2025-02-05, Last modification date: 2025-05-07) |
| Primary citation | Gandhivel, V.H.,Sotelo-Parrilla, P.,Raju, S.,Jha, S.,Gireesh, A.,Harshith, C.Y.,Gut, F.,Vinothkumar, K.R.,Berger, F.,Jeyaprakash, A.A.,Shivaprasad, P.V. An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses. Nat.Plants, 11:790-807, 2025 Cited by PubMed Abstract: Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the mechanism of action and functional significance of several variants of core histones are well known except those of histone H4. Here we show that a variant of H4 (H4.V) expressing tissue-specifically among Oryza members mediated specific epigenetic changes contributing to salt tolerance. H4.V was incorporated into specific heterochromatic sites, where it blocked the deposition of active histone marks. Stress-dependent redistribution of H4.V enabled the incorporation of acetylated H4 lysine 5 (H4K5ac) in the gene bodies. The misexpression of H4.V led to defects in reproductive development and in mounting salt stress responses. H4.V formed homotypic nucleosomes and mediated these alterations by conferring distinct molecular properties to the nucleosomes, as seen with cryo electron microscopy structures and biochemical assays. These results reveal not only an H4 variant among plants but also a chromatin regulation that might have contributed to the adaptation of semi-aquatic Oryza members. PubMed: 40200022DOI: 10.1038/s41477-025-01974-2 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.6 Å) |
Structure validation
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