9EXS

Cryo-EM structure of Ch. thermophilum Rai1-Rat1 dimer.

Summary for 9EXS

• Entry DOI: 10.2210/pdb9exs/pdb
• Related: 8Q6V
• EMDB information: 18199 50048
• Descriptor: Decapping nuclease, 5'-3' exoribonuclease, MAGNESIUM ION (3 entities in total)
• Functional Keywords: rai1 nuclease, rtt103 binding, structured, rna binding, rna binding protein
• Biological source: Thermochaetoides thermophila; More
• Total number of polymer chains: 2
• Total formula weight: 166177.71

Authors

Noskova, N.,Dikunova, A.,Stefl, R. (deposition date: 2024-04-08, release date: 2024-12-18, Last modification date: 2025-02-19)

Primary citation

Dikunova, A.,Noskova, N.,Overbeck, J.H.,Polak, M.,Stelzig, D.,Zapletal, D.,Kubicek, K.,Novacek, J.,Sprangers, R.,Stefl, R.
Assembly of the Xrn2/Rat1-Rai1-Rtt103 termination complexes in mesophilic and thermophilic organisms.
Structure, 33:300-, 2025

PubMed Abstract: The 5'-3' exoribonuclease Xrn2, known as Rat1 in yeasts, terminates mRNA transcription by RNA polymerase II (RNAPII). In the torpedo model of termination, the activity of Xrn2/Rat1 is enhanced by Rai1, which is recruited to the termination site by Rtt103, an adaptor protein binding to the RNAPII C-terminal domain (CTD). The overall architecture of the Xrn2/Rat1-Rai1-Rtt103 complex remains unknown. We combined structural biology methods to characterize the torpedo complex from Saccharomyces cerevisiae and Chaetomium thermophilum. Comparison of the structures from these organisms revealed a conserved protein core fold of the subunits, but significant variability in their interaction interfaces. We found that in the mesophile, Rtt103 utilizes an unstructured region to augment a Rai1 β-sheet, while in the thermophile Rtt103 binds to a C-terminal helix of Rai1 via its CTD-interacting domain with an α-helical fold. These different torpedo complex assemblies reflect adaptations to the environment and impact complex recruitment to RNAPII.

PubMed: 39657659
DOI: 10.1016/j.str.2024.11.010

Experimental method

ELECTRON MICROSCOPY (3.28 Å)