9V4M

Crystal structure of the T.thermophilus transcription initiation complex bound to Ap4G

This is a non-PDB format compatible entry.

Summary for 9V4M

• Entry DOI: 10.2210/pdb9v4m/pdb
• Related: 9UPW
• Descriptor: DNA-directed RNA polymerase subunit alpha, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ZINC ION, ... (12 entities in total)
• Functional Keywords: complex, transcription
• Biological source: Thermus thermophilus HB8; More
• Total number of polymer chains: 8
• Total formula weight: 445424.63

Authors

Duan, W.,Kaushik, A.,Serganov, A. (deposition date: 2025-05-24, release date: 2025-10-22, Last modification date: 2025-10-29)

Primary citation

Duan, W.,Kaushik, A.,Unarta, I.C.,Wu, Y.,Liu, M.M.J.,Weaver, J.W.,Wang, B.,Rice, W.J.,Luciano, D.J.,Belasco, J.G.,Huang, X.,Nudler, E.,Serganov, A.
Molecular basis for noncanonical transcription initiation from Np 4 A alarmones.
Nat.Chem.Biol., 2025

PubMed Abstract: Stress-induced dinucleoside tetraphosphates (NpNs, where N is adenosine, guanosine, cytosine or uridine) are ubiquitous in living organisms, yet their function has been largely elusive for over 50 years. Recent studies have revealed that RNA polymerase can influence the cellular lifetime of transcripts by incorporating these alarmones into RNA as 5'-terminal caps. Here we present structural and biochemical data that reveal the molecular basis of noncanonical transcription initiation from NpAs by Escherichia coli and Thermus thermophilus RNA polymerases. Our results show the influence of the first two nucleotide incorporation steps on capping efficiency and the different interactions of NpAs with transcription initiation complexes. These data provide critical insights into the substrate selectivity that dictates levels of Np capping in bacterial cells.

PubMed: 41094128
DOI: 10.1038/s41589-025-02044-6

Experimental method

X-RAY DIFFRACTION (3 Å)