9R75
Transcription initiation T. thermophilus RNA polymerase complex with anti-scrunched TC DNA template
Summary for 9R75
| Entry DOI | 10.2210/pdb9r75/pdb |
| Related | 9FO6 |
| EMDB information | 50618 53711 |
| Descriptor | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... (9 entities in total) |
| Functional Keywords | transcription-dna complex, non-canonical cap, transcription |
| Biological source | Thermus thermophilus HB8 More |
| Total number of polymer chains | 8 |
| Total formula weight | 462555.16 |
| Authors | Skerlova, J.,Dubankova, A.,Svachova, H.,Kouba, T. (deposition date: 2025-05-13, release date: 2025-12-17, Last modification date: 2026-01-21) |
| Primary citation | Serianni, V.M.,Skerlova, J.,Dubankova, A.K.,Skriba, A.,Svachova, H.,Vuckova, T.,Filimonenko, A.,Fabry, M.,Rezacova, P.,Kouba, T.,Cahova, H. Molecular insight into 5' RNA capping with Np n Ns by bacterial RNA polymerase. Nat.Chem.Biol., 2026 Cited by PubMed Abstract: RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside polyphosphates by RNA polymerase as noncanonical initiating nucleotides. However, how these compounds bind into the active site of RNA polymerase during transcription initiation is unknown. Here, we explored transcription initiation in vitro, using a series of DNA templates in combination with dinucleoside polyphosphates and model RNA polymerase from Thermus thermophilus. We observed that the transcription start site can vary on the basis of the compatibility of the specific template and dinucleoside polyphosphate. Cryo-electron microscopy structures of transcription initiation complexes with dinucleoside polyphosphates revealed that both nucleobase moieties can pair with the DNA template. The first encoded nucleotide pairs in a canonical Watson-Crick manner, whereas the second nucleobase pairs noncanonically in a reverse Watson-Crick manner. Our work provides a structural explanation of how dinucleoside polyphosphates initiate RNA transcription. PubMed: 41513851DOI: 10.1038/s41589-025-02134-5 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.8 Å) |
Structure validation
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