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	Real-time capture of σ transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 7138, Year 2025
Publish date	Aug 4, 2025
Authors	Andreas U Mueller / Nina Molina / B Tracy Nixon / Seth A Darst /
PubMed Abstract	Bacterial σ factors bind RNA polymerase (E) to form holoenzyme (Eσ), conferring promoter specificity to E and playing a key role in transcription bubble formation. σ is unique among σ factors in ...Bacterial σ factors bind RNA polymerase (E) to form holoenzyme (Eσ), conferring promoter specificity to E and playing a key role in transcription bubble formation. σ is unique among σ factors in its structure and functional mechanism, requiring activation by specialized AAA+ ATPases. Eσ forms an inactive promoter complex where the N-terminal σ region I (σ-RI) threads through a small DNA bubble. On the opposite side of the DNA, the ATPase engages σ-RI within the pore of its hexameric ring. Here, we perform kinetics-guided structural analysis of de novo formed Eσ initiation complexes and engineer a biochemical assay to measure ATPase-mediated σ-RI translocation during promoter melting. We show that the ATPase exerts mechanical action to translocate about 30 residues of σ-RI through the DNA bubble, disrupting inhibitory structures of σ to allow full transcription bubble formation. A local charge switch of σ-RI from positive to negative may help facilitate disengagement of the otherwise processive ATPase, allowing subsequent σ disentanglement from the DNA bubble.
External links	Nat Commun / PubMed:40759887 / PubMed Central
Methods	EM (single particle)
Resolution	2.6 - 4.6 Å
Structure data	EMDB-48574: Mycobacterial open-gate proteasome in complex with engineered NtrC1 Method: EM (single particle) / Resolution: 4.6 Å EMDB-48576: de novo SigN RNA polymerase open complex (RPo), consensus map Method: EM (single particle) / Resolution: 2.8 Å EMDB-48577: de novo SigN RNA polymerase open complex (RPo), SigN focus map Method: EM (single particle) / Resolution: 3.2 Å EMDB-48578: de novo SigN RNA polymerase NTP-bound open complex (RPo+2A), consensus map Method: EM (single particle) / Resolution: 3.1 Å EMDB-48579: de novo SigN RNA polymerase NTP-bound open complex (RPo+2A), SigN focus map Method: EM (single particle) / Resolution: 3.6 Å EMDB-48580: de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring), consensus map Method: EM (single particle) / Resolution: 2.7 Å EMDB-48581: de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring), SigN focus map Method: EM (single particle) / Resolution: 3.1 Å EMDB-48582: de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring), bEBP focus map Method: EM (single particle) / Resolution: 3.1 Å EMDB-48583: de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring), consensus map Method: EM (single particle) / Resolution: 2.6 Å EMDB-48584: de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring), SigN focus map Method: EM (single particle) / Resolution: 3.0 Å EMDB-48585: de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring), bEBP focus map Method: EM (single particle) / Resolution: 3.0 Å 48586 9mse EMDB-48586, PDB-9mse: de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring) Method: EM (single particle) / Resolution: 2.7 Å 48587 9msf EMDB-48587, PDB-9msf: de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring) Method: EM (single particle) / Resolution: 2.6 Å 48588 9msg EMDB-48588, PDB-9msg: De novo SigN RNA polymerase transcription initiation intermediate with bound SigN-RII Method: EM (single particle) / Resolution: 2.7 Å 48589 9msh EMDB-48589, PDB-9msh: de novo SigN RNA polymerase open complex (RPo) Method: EM (single particle) / Resolution: 2.8 Å 48590 9msj EMDB-48590, PDB-9msj: de novo SigN RNA polymerase NTP-bound open complex (RPo+2A) Method: EM (single particle) / Resolution: 3.1 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-POP: PYROPHOSPHATE 2- ChemComp-ZN: Unknown entry ChemComp-HOH: WATER ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM
Source	escherichia coli (E. coli) aquifex aeolicus vf5 (bacteria) Mycobacterium tuberculosis H37Rv (bacteria)
Keywords	TRANSCRIPTION / sigma N / sigma 54 / ATPase / bacterial enhancer binding protein / transcription initiation / intermediate / TRANSFERASE/DNA / TRANSFERASE-DNA complex