29WD

RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome

This is a non-PDB format compatible entry.

Summary for 29WD

• Entry DOI: 10.2210/pdb29wd/pdb
• EMDB information: 57401
• Descriptor: General transcription and DNA repair factor IIH helicase subunit XPB, Cyclin-H, DNA-directed RNA polymerase subunit, ... (42 entities in total)
• Functional Keywords: rna polymerase ii, transcription
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 40
• Total formula weight: 1584063.28

Authors

Zhan, Y.,Abril-Garrido, J.,Dienemann, C.,Cramer, P. (deposition date: 2026-04-10, release date: 2026-07-22, Last modification date: 2026-09-02)

Primary citation

Zhan, Y.,Abril-Garrido, J.,Grabbe, F.,Seweryn, P.,Neef, U.,Dienemann, C.,Cramer, P.
The +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation.
Mol.Cell, 86:2939-, 2026

PubMed Abstract: Transcription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre-initiation complex (PIC) assembly and RNA Pol II pausing, but its function in transcription initiation and the transition to elongation remains unclear. Here, we investigate the transcription initiation-elongation transition in vitro using DNA templates containing a +1 nucleosome and present cryo-electron microscopy (cryo-EM) structures of five intermediate states. First, after PIC assembly, ATP binding to TFIIH enables the +1 nucleosome to evict TFIID from the PIC. Following DNA opening, the +1 nucleosome stimulates TFIIH translocase activity and initial RNA synthesis. Finally, after DNA bubble rewinding, the +1 nucleosome removes TFIIH from the early elongation complex for promoter escape. Our findings show that the +1 nucleosome not only acts passively in PIC assembly and RNA Pol II pausing but rather has active functions during the initiation-elongation transition of transcription.

PubMed: 42480520
DOI: 10.1016/j.molcel.2026.06.042

Experimental method

ELECTRON MICROSCOPY (4.2 Å)