Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation.
Journal, issue, pages	Nat Struct Mol Biol, Year 2025
Publish date	Dec 1, 2025
Authors	Vita Vidmar / Céline Borde / Lisa Bruno / Nataliya Miropolskaya / Maria Takacs / Claire Batisse / Charlotte Saint-André / Chengjin Zhu / Olivier Espéli / Valérie Lamour / Albert Weixlbaumer /
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 ...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.
External links	Nat Struct Mol Biol / PubMed:41326756
Methods	EM (single particle)
Resolution	2.6 - 5.6 Å
Structure data	EMDB-51252: RNAP-TopoI complex on duplex scaffold - consensus map Method: EM (single particle) / Resolution: 2.7 Å EMDB-51253: RNAP-TopoI complex on duplex scaffold - focused map (TopoI) Method: EM (single particle) / Resolution: 3.3 Å EMDB-51254: RNAP-TopoI complex on duplex scaffold - focused map (TopoI D2/D3) Method: EM (single particle) / Resolution: 3.4 Å EMDB-51255: RNAP-TopoI complex on duplex scaffold - focused map (RNAP core) Method: EM (single particle) / Resolution: 2.6 Å EMDB-51256: RNAP-TopoI complex on duplex scaffold - focused map (RNAP swivel module 1) Method: EM (single particle) / Resolution: 2.7 Å EMDB-51257: RNAP-TopoI complex on duplex scaffold - focused map (RNAP swivel module 2) Method: EM (single particle) / Resolution: 2.7 Å EMDB-51258: RNAP-TopoI complex on duplex scaffold - focused map (RNAP beta protrusion and lobe) Method: EM (single particle) / Resolution: 2.8 Å 51259 9gda EMDB-51259, PDB-9gda: RNAP-TopoI complex on duplex scaffold Method: EM (single particle) / Resolution: 2.7 Å 51260 9gdb EMDB-51260, PDB-9gdb: RNAP-TopoI complex on bubble scaffold - consensus reconstruction Method: EM (single particle) / Resolution: 3.8 Å 51261 9gdc EMDB-51261, PDB-9gdc: RNAP-TopoI complex on bubble scaffold - single-bubble configuration Method: EM (single particle) / Resolution: 4.3 Å 51262 9gdd EMDB-51262, PDB-9gdd: RNAP-TopoI complex on bubble scaffold - two-bubble configuration Method: EM (single particle) / Resolution: 4.3 Å 51263 9gde EMDB-51263, PDB-9gde: RNAP-TopoI complex on long-overhang scaffold - orientation 1 Method: EM (single particle) / Resolution: 4.0 Å 51264 9gdh EMDB-51264, PDB-9gdh: RNAP-TopoI complex on long-overhang scaffold - orientation 2 Method: EM (single particle) / Resolution: 3.9 Å EMDB-51265: RNAP-TopoI complex on duplex scaffold with visible TOPRIM loop - consensus map Method: EM (single particle) / Resolution: 2.8 Å EMDB-51266: RNAP-TopoI complex on duplex scaffold with visible TOPRIM loop - focused map (TopoI) Method: EM (single particle) / Resolution: 3.8 Å EMDB-51267: RNAP-TopoI complex on duplex scaffold with visible TOPRIM loop Method: EM (single particle) / Resolution: 3.8 Å EMDB-51268: RNAP-TopoI complex on long-overhang scaffold - orientation 3 Method: EM (single particle) / Resolution: 5.6 Å EMDB-51269: RNAP-TopoI complex on long-overhang scaffold - TopoI gate opening (orientation 2) Method: EM (single particle) / Resolution: 4.3 Å EMDB-51270: RNAP-TopoI complex on short-overhang scaffold - orientation 1 Method: EM (single particle) / Resolution: 3.8 Å EMDB-51271: RNAP-TopoI complex on short-overhang scaffold - orientation 2 Method: EM (single particle) / Resolution: 4.4 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry
Source	escherichia coli (E. coli) synthetic construct (others)
Keywords	TRANSCRIPTION / RNA polymerase / topoisomerase / DNA topology