9II7
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B
Summary for 9II7
| Entry DOI | 10.2210/pdb9ii7/pdb |
| EMDB information | 60593 |
| 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, ... (24 entities in total) |
| Functional Keywords | transcription-dna-rna complex, rnapii, transcription |
| Biological source | Komagataella phaffii More |
| Total number of polymer chains | 24 |
| Total formula weight | 844875.12 |
| Authors | Akatsu, M.,Kujirai, T.,Rina, H.,Ehara, H.,Takizawa, Y.,Sekine, S.,Kurumizaka, H. (deposition date: 2024-06-19, release date: 2025-06-11) |
| Primary citation | Akatsu, M.,Hirano, R.,Kujirai, T.,Ogasawara, M.,Ehara, H.,Sekine, S.I.,Takizawa, Y.,Kurumizaka, H. Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B. Embo J., 2025 Cited by PubMed Abstract: H2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that the RNA polymerase II elongation complex (EC) transcribes the nucleosome containing H2A.B more efficiently than that with canonical H2A in vitro. Our cryo-electron microscopy analysis of the H2A.B nucleosome during transcription revealed that the proximal H2A.B-H2B dimer is released from the nucleosome as the EC transcribes the proximal half of the nucleosomal DNA. This dissociation, which is not observed in the canonical H2A nucleosome, likely enhances the EC elongation efficiency in the H2A.B nucleosome. Mutational analyses suggested that the unique short C-terminal region of H2A.B alone enhances EC elongation efficiency when substituted for its counterpart in canonical H2A. Additionally, other regions of H2A.B contribute to this enhancement. These structural and biochemical findings provide new insights into the role of H2A.B in regulating gene expression. PubMed: 40447801DOI: 10.1038/s44318-025-00473-6 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.5 Å) |
Structure validation
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