9GDD
RNAP-TopoI complex on bubble scaffold - two-bubble configuration
This is a non-PDB format compatible entry.
Summary for 9GDD
| Entry DOI | 10.2210/pdb9gdd/pdb |
| Related | 9GDA 9GDB 9GDC |
| EMDB information | 51259 51260 51261 51262 |
| Descriptor | DNA-directed RNA polymerase subunit alpha, ZINC ION, DNA-directed RNA polymerase subunit beta, ... (10 entities in total) |
| Functional Keywords | rna polymerase, topoisomerase, dna topology, transcription |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 9 |
| Total formula weight | 528601.04 |
| Authors | Vidmar, V.,Weixlbaumer, A.,Lamour, V. (deposition date: 2024-08-05, release date: 2025-11-05, Last modification date: 2025-12-17) |
| Primary citation | Vidmar, V.,Borde, C.,Bruno, L.,Miropolskaya, N.,Takacs, M.,Batisse, C.,Saint-Andre, C.,Zhu, C.,Espeli, O.,Lamour, V.,Weixlbaumer, A. DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation. Nat.Struct.Mol.Biol., 2025 Cited by PubMed Abstract: During transcription, RNA polymerase (RNAP) continuously unwinds and rewinds DNA, generating negative and positive supercoils upstream and downstream, respectively. Using single-particle cryo-EM, we elucidated how bacterial RNAP and DNA topoisomerase I (TopoI), which relaxes negative supercoils, operate in close spatial proximity. TopoI binds to relaxed DNA upstream of RNAP, and this involves a conformational switch in the TopoI functional domains. This suggests that TopoI exerts a sensing role before the formation of negative supercoils. On DNA substrates mimicking negatively supercoiled DNA, TopoI threads one strand into the active site for cleavage and binds the complementary strand with an auxiliary domain. Transcriptomic and phenotypic analyses suggest that mutations affecting conformational changes in TopoI impact gene expression and operon polarity in bacteria. In summary, we propose a comprehensive model for DNA relaxation in the proximity of active bacterial transcription. PubMed: 41326756DOI: 10.1038/s41594-025-01703-5 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (4.3 Å) |
Structure validation
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