9W74
Cryo-EM structure of the close-packed di-hexasome (CPDH)
Summary for 9W74
| Entry DOI | 10.2210/pdb9w74/pdb |
| EMDB information | 65715 65716 |
| Descriptor | Histone H3.2, Histone H4, Histone H2A type 1, ... (6 entities in total) |
| Functional Keywords | chromatin, nucleosome, hexasome, subnucleosome, histone, dna, gene regulation |
| Biological source | Xenopus laevis (African clawed frog) More |
| Total number of polymer chains | 14 |
| Total formula weight | 306168.08 |
| Authors | Ho, C.-H.,Takizawa, Y.,Kurumizaka, H. (deposition date: 2025-08-05, release date: 2025-12-10, Last modification date: 2026-01-28) |
| Primary citation | Ho, C.H.,Kobayashi, Y.,Ogasawara, M.,Takizawa, Y.,Kurumizaka, H. A method for cryo-EM analysis of eukaryotic nucleosomes reconstituted in bacterial cells. Iscience, 29:114453-114453, 2026 Cited by PubMed Abstract: Conventional methods for preparing nucleosomes are time-consuming and technically demanding. In the present study, we extended the approach of generating nucleosomes in by the co-expression of all four histones, allowing nucleosomes to be assembled in cells. The bacterially reconstituted nucleosomes can be readily prepared from the cells and directly subjected to cryo-EM single particle analysis. Using this method, we obtained a 2.56 Å nucleosome structure that is highly similar to a previously reported nucleosome crystal structure, validating the use of nucleosomes formed in for cryo-EM analysis. Unexpectedly, we also discovered a non-canonical nucleosome structure, in which two hexasomes are closely packed. This system provides a robust and efficient platform for structural studies of nucleosomes and nucleosome variants, and may facilitate the discovery of chromatin architectures. PubMed: 41541688DOI: 10.1016/j.isci.2025.114453 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (4.94 Å) |
Structure validation
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