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	Cryo-EM uncovers a sequential mechanism for RNA polymerase I pausing and stalling at abasic DNA lesions.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 5254, Year 2025
Publish date	Jun 6, 2025
Authors	Alicia Santos-Aledo / Adrián Plaza-Pegueroles / Marta Sanz-Murillo / Federico M Ruiz / Peini Hou / Jun Xu / David Gil-Carton / Dong Wang / Carlos Fernández-Tornero /
PubMed Abstract	During synthesis of the ribosomal RNA precursor, RNA polymerase I (Pol I) monitors DNA integrity but its response to DNA damage remains poorly studied. Abasic sites are among the most prevalent DNA ...During synthesis of the ribosomal RNA precursor, RNA polymerase I (Pol I) monitors DNA integrity but its response to DNA damage remains poorly studied. Abasic sites are among the most prevalent DNA lesions in eukaryotic cells, and their detection is critical for cell survival. We report cryo-EM structures of Pol I in different stages of stalling at abasic sites, supported by in vitro transcription studies. Slow nucleotide addition opposite abasic sites occurs through base sandwiching between the RNA 3'-end and the Pol I bridge helix. Templating abasic sites can also cause Pol I cleft opening, which enables the A12 subunit to access the active center. Nucleotide addition opposite the lesion induces a translocation intermediate where DNA bases tilt to form hydrogen bonds with the new RNA base. These findings reveal unique mechanisms of Pol I stalling at abasic sites, differing from arrest by bulky lesions or abasic site handling by RNA polymerase II.
External links	Nat Commun / PubMed:40480971 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 3.5 Å
Structure data	50955 9g1v EMDB-50955, PDB-9g1v: Yeast RNA polymerase I elongation complex stalled by an apurinic site Method: EM (single particle) / Resolution: 2.7 Å 50956 9g1x EMDB-50956, PDB-9g1x: Yeast RNA polymerase I elongation complex stalled by an apurinic site, 11-subunit Method: EM (single particle) / Resolution: 3.5 Å 50962 9g23 EMDB-50962, PDB-9g23: Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at A-site Method: EM (single particle) / Resolution: 3.4 Å 50963 9g24 EMDB-50963, PDB-9g24: Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at E-site Method: EM (single particle) / Resolution: 3.5 Å 50965 9g26 EMDB-50965, PDB-9g26: Yeast RNA polymerase I elongation complex stalled by an apurinic site, closed state Method: EM (single particle) / Resolution: 3.4 Å 50966 9g27 EMDB-50966, PDB-9g27: Yeast RNA polymerase I elongation complex stalled by an apurinic site, pre-translocation state Method: EM (single particle) / Resolution: 2.8 Å 50970 9g29 EMDB-50970, PDB-9g29: Yeast RNA polymerase I elongation complex stalled by an apurinic site with the C-terminal of A12 in the funnel Method: EM (single particle) / Resolution: 3.3 Å 50971 9g2b EMDB-50971, PDB-9g2b: Yeast RNA polymerase I elongation complex stalled by an apurinic site, 12-subunit Method: EM (single particle) / Resolution: 3.2 Å 50972 9g2c EMDB-50972, PDB-9g2c: Yeast RNA polymerase I elongation complex stalled by an apurinic site, open state Method: EM (single particle) / Resolution: 3.5 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / AMP-CPP, energy-carrying molecule analogue*YM
Source	saccharomyces cerevisiae (brewer's yeast)
Keywords	TRANSCRIPTION / DNA lesion