9J0P
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc)
Summary for 9J0P
| Entry DOI | 10.2210/pdb9j0p/pdb |
| EMDB information | 61060 |
| Descriptor | DNA-directed RNA polymerase subunit, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, ... (27 entities in total) |
| Functional Keywords | rna polymerase, nelf, nucleosome, dna, rna, transcription |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 29 |
| Total formula weight | 1128676.57 |
| Authors | Naganuma, M.,Kujirai, T.,Ehara, H.,Uejima, T.,Ito, T.,Goto, M.,Aoki, M.,Henmi, M.,Miyamoto-Kohno, S.,Shirouzu, M.,Kurumizaka, H.,Sekine, S. (deposition date: 2024-08-02, release date: 2025-02-05, Last modification date: 2025-03-19) |
| Primary citation | Naganuma, M.,Kujirai, T.,Ehara, H.,Uejima, T.,Ito, T.,Goto, M.,Aoki, M.,Henmi, M.,Miyamoto-Kohno, S.,Shirouzu, M.,Kurumizaka, H.,Sekine, S.I. Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome. Sci Adv, 11:eadu0577-eadu0577, 2025 Cited by PubMed Abstract: The metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing involves negative elongation factor (NELF), 5,6-dichloro-1-β-d-ribobenzimidazole sensitivity-inducing factor (DSIF), and transcription elongation factor IIS (TFIIS) and is critical for subsequent productive transcription elongation. However, the detailed pausing mechanism and the involvement of the +1 nucleosome remain enigmatic. Here, we report cryo-electron microscopy structures of ECs stalled on nucleosomal DNA. In the absence of TFIIS, the EC is backtracked/arrested due to conflicts between NELF and the nucleosome. We identified two alternative binding modes of NELF, one of which reveals a critical contact with the downstream DNA through the conserved NELF-E basic helix. Upon binding with TFIIS, the EC progressed to the nucleosome to establish a paused EC with a partially unwrapped nucleosome. This paused EC strongly restricts EC progression further downstream. These structures illuminate the mechanism of RNAPII pausing/stalling at the +1 nucleosome. PubMed: 40043114DOI: 10.1126/sciadv.adu0577 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.3 Å) |
Structure validation
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