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	Molecular insight into 5' RNA capping with NpNs by bacterial RNA polymerase.
Journal, issue, pages	Nat Chem Biol, Year 2026
Publish date	Jan 9, 2026
Authors	Valentina M Serianni / Jana Škerlová / Anna Knopp Dubánková / Anton Škríba / Hana Šváchová / Tereza Vučková / Anatolij Filimoněnko / Milan Fábry / Pavlína Řezáčová / Tomáš Kouba / Hana Cahova
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 ...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.
External links	Nat Chem Biol / PubMed:41513851
Methods	EM (single particle)
Resolution	2.42 - 3.8 Å
Structure data	50618 9fo6 EMDB-50618, PDB-9fo6: GTP bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template Method: EM (single particle) / Resolution: 2.76 Å 50622 9fog EMDB-50622, PDB-9fog: Ap3G bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template Method: EM (single particle) / Resolution: 2.51 Å 50625 9fok EMDB-50625, PDB-9fok: Ap4G bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template Method: EM (single particle) / Resolution: 3.0 Å 50634 9fp3 EMDB-50634, PDB-9fp3: Ap4A bound in de novo transcription initiation T. thermophilus RNA polymerase complex with TC DNA template Method: EM (single particle) / Resolution: 2.42 Å 50715 9frj EMDB-50715, PDB-9frj: Ap4A bound in de novo transcription initiation T. thermophilus RNA polymerase complex with aTT DNA template Method: EM (single particle) / Resolution: 2.66 Å 53711 9r75 EMDB-53711, PDB-9r75: Transcription initiation T. thermophilus RNA polymerase complex with anti-scrunched TC DNA template Method: EM (single particle) / Resolution: 3.8 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM ChemComp-2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine ChemComp-G3A: GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE PDB-1if9: Carbonic Anhydrase II Complexed With N-[2-(1H-Indol-5-yl)-butyl]-4-sulfamoyl-benzamide ChemComp-B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE ChemComp-G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogueYM
Source	thermus thermophilus hb8 (bacteria) synthetic construct (others)
Keywords	TRANSCRIPTION / TRANSCRIPTION-DNA complex / non-canonical cap