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	RNA polymerase inhibitors reveal active-site motions essential for the nucleotide addition cycle.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 123, Issue 27, Page e2609228123, Year 2026
Publish date	Jul 7, 2026
Authors	Yukti Dhingra / Robert Landick / Elizabeth A Campbell / Seth A Darst /
PubMed Abstract	The nucleotide addition cycle (NAC) of multisubunit DNA-dependent RNA polymerases (RNAPs) involves coordinated conformational changes in conserved active-site structural elements, including the ...The nucleotide addition cycle (NAC) of multisubunit DNA-dependent RNA polymerases (RNAPs) involves coordinated conformational changes in conserved active-site structural elements, including the trigger loop (TL). The TL is open (unfolded) in most RNAP structures but can close (fold) in substrate-bound (post- or pretranslocated) states of the RNAP, promoting catalysis. TL closure has been associated with closure of another conserved structural element, the Rim-Helices/F-loop (RH-FL), but the role of the RH-FL in the NAC is unclear. Antibiotic leads CBR9379 and AAP-SO inhibit the and RNAPs, respectively, by binding in a pocket formed by the bridge helix and RH-FL. The precise mechanism of action for these inhibitors is yet to be defined. We present cryoelectron microscopy structures showing that both compounds inhibit the RNAP NAC by preventing RH-FL closure, thereby allosterically destabilizing the closed TL. This work reveals a conserved mechanistic principle of RNAP catalysis across all domains of life and provides insight for antibiotic design.
External links	Proc Natl Acad Sci U S A / PubMed:42378287 / PubMed Central
Methods	EM (single particle)
Resolution	2.8 - 4.0 Å
Structure data	75279 10ma EMDB-75279, PDB-10ma: Closed Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with a closed active site (closed TL, SI3 and RH-FL) Method: EM (single particle) / Resolution: 2.9 Å 75280 10mb EMDB-75280, PDB-10mb: Open1 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL) Method: EM (single particle) / Resolution: 2.9 Å 75281 10mc EMDB-75281, PDB-10mc: Open2 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL) Method: EM (single particle) / Resolution: 2.8 Å 75282 10md EMDB-75282, PDB-10md: Open3 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL) Method: EM (single particle) / Resolution: 2.8 Å 75283 10me EMDB-75283, PDB-10me: SemiClosed Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with a semi-closed active site (closed TL and SI3, open RH-FL) Method: EM (single particle) / Resolution: 4.0 Å 75284 10mf EMDB-75284, PDB-10mf: CBR9379 bound Open1 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL) Method: EM (single particle) / Resolution: 2.8 Å 75285 10mg EMDB-75285, PDB-10mg: CBR9379 bound Open2 Eco-ePEC: Cryo-EM structure of Eco RNAP his-elemental paused elongation complex with an open active site (open TL, SI3 and RH-FL) Method: EM (single particle) / Resolution: 2.9 Å 75286 10mi EMDB-75286, PDB-10mi: Closed Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with a closed active site (closed TL and RH-FL) Method: EM (single particle) / Resolution: 3.0 Å 75287 10mj EMDB-75287, PDB-10mj: Open Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with an open active site (open TL and RH-FL) Method: EM (single particle) / Resolution: 3.3 Å 75288 10mk EMDB-75288, PDB-10mk: SemiClosed Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with a semiclosed active site (closed TL, open RH-FL) Method: EM (single particle) / Resolution: 3.3 Å 75289 10ml EMDB-75289, PDB-10ml: AAP-SO2 bound Open Mtb-EC: Cryo-EM structure of Mtb RNAP elongation complex (substrate loading mimic) with an open active site (open TL and RH-FL) Method: EM (single particle) / Resolution: 3.0 Å
Chemicals	ChemComp-1N7: CHAPSO / detergentYM ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-HOH: WATER ChemComp-42T: 3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM PDB-1bnv: CARBONIC ANHYDRASE II INHIBITOR
Source	escherichia coli (E. coli) mycobacterium tuberculosis (bacteria)
Keywords	Transcription/DNA/RNA / Transcription / DNA/RNA / Nucleotide addition cycle / RNA polymerase / Transcription-DNA-RNA complex