SNAP output for PDB entry 8k5p [SNAP web server]

PDB-id

8k5p; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription

Method

cryo-EM (2.8 Å)

Summary

cryo-EM structure of yeast rat1-bound pol ii pre-termination transcription complex 2 (pol ii rat1-pttc2)

Reference

Zeng Y, Zhang HW, Wu XX, Zhang Y (2024): "Structural basis of exoribonuclease-mediated mRNA transcription termination." Nature. doi: 10.1038/s41586-024-07240-3.

Abstract

Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II)_1-5. Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5'-to-3' exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5' terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes.