9UJS

RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome

Summary for 9UJS

• Entry DOI: 10.2210/pdb9ujs/pdb
• Related: 9UJT
• EMDB information: 64225
• 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, ... (17 entities in total)
• Functional Keywords: rnapii, subnucleosome, transcription, transcription-rna-dna complex, transcription/rna/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 23
• Total formula weight: 745685.76

Authors

Ho, C.-H.,Nozawa, K.,Nishimura, M.,Oi, M.,Kujirai, T.,Ogasawara, M.,Ehara, H.,Sekine, S.,Takizawa, Y.,Kurumizaka, H. (deposition date: 2025-04-17, release date: 2026-04-15)

Primary citation

Ho, C.H.,Nozawa, K.,Nishimura, M.,Oi, M.,Kujirai, T.,Ogasawara, M.,Ehara, H.,Sekine, S.I.,Takizawa, Y.,Kurumizaka, H.
Structural basis of RNA polymerase II transcription on the histone H3-H4 octasome.
J.Biol.Chem., 302:111340-111340, 2026

PubMed Abstract: The histone H3-H4 octasome is a nucleosome-like particle in which two DNA gyres are wrapped around each histone (H3-H4) tetramer disk, forming a clamshell-like configuration. In the present study, we performed in vitro RNA polymerase II (RNAPII) transcription assays with the H3-H4 octasome and found that RNAPII transcribed the H3-H4 octasome more efficiently than the nucleosome. RNAPII paused at only one position, superhelical location (SHL(-4)) in the H3-H4 octasome, in contrast to pausing at the SHL(-5), SHL(-2), and SHL(-1) positions in the nucleosome. Cryo-EM analysis revealed that two (H3-H4) tetramer disks are retained when the RNAPII paused at the SHL(-4) position of the H3-H4 octasome. However, when RNAPII reached the SHL(-0.5) position, five base pairs before the dyad position of the H3-H4 octasome, the proximal (H3-H4) tetramer was disassembled, but the distal (H3-H4) tetramer still remained on the DNA. Therefore, RNAPII efficiently transcribes the H3-H4 octasome by stepwise (H3-H4) tetramer disassembly.

PubMed: 41791711
DOI: 10.1016/j.jbc.2026.111340

Experimental method

ELECTRON MICROSCOPY (3.62 Å)