8JH3
RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome
Summary for 8JH3
| Entry DOI | 10.2210/pdb8jh3/pdb |
| EMDB information | 36252 |
| 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-dna-rna complex, rnapii, transcription/dna/rna |
| Biological source | synthetic construct More |
| Total number of polymer chains | 23 |
| Total formula weight | 747091.58 |
| Authors | Akatsu, M.,Fujita, R.,Ogasawara, M.,Ehara, H.,Kujirai, T.,Takizawa, Y.,Sekine, S.,Kurumizaka, H. (deposition date: 2023-05-22, release date: 2023-11-29, Last modification date: 2023-12-20) |
| Primary citation | Akatsu, M.,Ehara, H.,Kujirai, T.,Fujita, R.,Ito, T.,Osumi, K.,Ogasawara, M.,Takizawa, Y.,Sekine, S.I.,Kurumizaka, H. Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. J.Biol.Chem., 299:105477-105477, 2023 Cited by PubMed Abstract: RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome. PubMed: 37981206DOI: 10.1016/j.jbc.2023.105477 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.7 Å) |
Structure validation
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