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	Structural basis of transcription-coupled RNA damage by incorporation of oxidized ribonucleotides.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 123, Issue 16, Page e2602266123, Year 2026
Publish date	Apr 21, 2026
Authors	Peini Hou / Chanjoo Lee / Jenny Chong / Juntaek Oh / Dong Wang /
PubMed Abstract	Oxidative stress induces damage to DNA, RNA, and nucleotide pools. Unlike well-studied DNA damage, the formation of RNA damage and the impact of an oxidized ribonucleotide pool on transcription ...Oxidative stress induces damage to DNA, RNA, and nucleotide pools. Unlike well-studied DNA damage, the formation of RNA damage and the impact of an oxidized ribonucleotide pool on transcription fidelity are poorly understood. Here, we investigate the structural basis of transcription-coupled RNA damage and the effect of 8-oxo-guanosine triphosphate (8-oxo-rGTP) on RNA polymerase II (Pol II) transcription fidelity control steps. We revealed that the incorporation efficiency of 8-oxo-rGTP opposite a dC template is comparable to that of GTP. In contrast, the incorporation efficiency of 8-oxo-rGTP opposite a dA template is ~150-fold more efficient than that of GTP. For the extension step, Pol II extends substantially faster from a 3'-8-oxo-rG:dC base pair than from a 3'-8-oxo-rG:dA base pair. For the proofreading step, strikingly, Pol II EC with 3'-8-oxo-rG:dA base pair is much more resistant to backtracking and proofreading than Pol II EC with 3'-8-oxo-rG:dC base pair. Using X-ray crystallography, we revealed that 8-oxo-rGTP adopts different prechemistry binding sites depending on whether it is paired with a dC or a dA template. Upon incorporation, the nucleobase of 8-oxo-rG flips to the -conformation to form a Hoogsteen pair with a dA template, whereas it remains in the -conformation to form a Watson-Crick pair with a dC template. Collectively, our work demonstrates that nucleotide-pool oxidation can directly affect Pol II fidelity control steps and elongation dynamics and induce RNA damage in a transcription-coupled manner.
External links	Proc Natl Acad Sci U S A / PubMed:41980106 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.39 - 3.68 Å
Structure data	71877 9puv EMDB-71877, PDB-9puv: Insulin receptor bound to S961 Method: EM (single particle) / Resolution: 3.68 Å PDB-9pvv: RNA polymerase II elongation complex with dC at +1 site, 8-oxo-GTP bound in A-site. Method: X-RAY DIFFRACTION / Resolution: 3.48 Å PDB-9pvw: RNA polymerase II elongation complex with dA at +1 site, 8-oxo-GMP added in Syn-conformation Method: X-RAY DIFFRACTION / Resolution: 3.56 Å PDB-9pvx: RNA polymerase II elongation complex with dA at +1 site, 8-oxo-GTP bound in E-site. Method: X-RAY DIFFRACTION / Resolution: 3.39 Å
Chemicals	ChemComp-8GT: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE ChemComp-ZN: Unknown entry ChemComp-MG: Unknown entry ChemComp-POP: PYROPHOSPHATE 2-
Source	homo sapiens (human) phage #d (virus) saccharomyces cerevisiae s288c (yeast) synthetic construct (others)
Keywords	MEMBRANE PROTEIN / Antagonist / receptor tyrosine kinase / TRANSCRIPTION / RNA polymerase II / oxidative damage / in vitro transcription / 8-oxoguanine