9UXW
RNA polymerase II elongation complex stalled at SHL(-0.5) in the hexasome of the overlapping dinucleosome
This is a non-PDB format compatible entry.
Summary for 9UXW
| Entry DOI | 10.2210/pdb9uxw/pdb |
| EMDB information | 64603 |
| Descriptor | DNA-directed RNA polymerase subunit, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, ... (21 entities in total) |
| Functional Keywords | transcription, chromatin, rna polymerase ii, overlapping dinucleosome |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 29 |
| Total formula weight | 867378.90 |
| Authors | Chen, Z.,Ho, C.,Tanaka, H.,Kujirai, T.,Ogasawara, M.,Ehara, H.,Sekine, S.,Takizawa, Y.,Kurumizaka, H. (deposition date: 2025-05-14, release date: 2026-07-01, Last modification date: 2026-07-29) |
| Primary citation | Chen, Z.,Ho, C.H.,Tanaka, H.,Kujirai, T.,Ogasawara, M.,Ehara, H.,Sekine, S.I.,Takizawa, Y.,Kurumizaka, H. Structural basis of asymmetric transcription through a composite nucleosome formed by a hexasome and an octasome. Nat.Struct.Mol.Biol., 33:1097-1104, 2026 Cited by PubMed Abstract: The overlapping dinucleosome (OLDN), a composite chromatin particle consisting of a hexasome and a canonical octasome, forms immediately downstream of transcription start sites, probably through chromatin remodeling activity, and has been proposed to act as a transient regulatory intermediate during transcription. Nevertheless, how RNA polymerase II (RNAPII) engages with and transcribes through this unusual structure has remained unclear. Here we reconstituted OLDNs in vitro and performed transcription assays with RNAPII. We found that transcription efficiency was markedly higher when RNAPII initiated from the hexasome side than from the octasome side. Cryo-electron microscopy further revealed that transcription from the hexasome side induced pronounced conformational rearrangements, in which RNAPII progression dramatically opened the hexasome-octasome interface. These results identify a mechanism by which RNAPII senses the intrinsic transcriptional polarity of OLDNs and suggest that OLDNs function as dynamic, directionally sensitive regulators of transcription elongation. PubMed: 42350665DOI: 10.1038/s41594-026-01837-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.74 Å) |
Structure validation
Download full validation report
