8YFR

Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft

Summary for 8YFR

• Entry DOI: 10.2210/pdb8yfr/pdb
• Related: 8YF5 8YFE 8YFQ
• EMDB information: 39211 39221 39226 39227
• Descriptor: DNA-directed RNA polymerase subunit, RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III, RNA polymerase II subunit B12.5, ... (16 entities in total)
• Functional Keywords: transcription termination, rna polymerase ii, transcription
• Biological source: Komagataella phaffii; More
• Total number of polymer chains: 14
• Total formula weight: 670913.36

Authors

Murayama, Y.,Yanagisawa, T.,Ehara, H.,Sekine, S. (deposition date: 2024-02-25, release date: 2024-09-25)

Primary citation

Yanagisawa, T.,Murayama, Y.,Ehara, H.,Goto, M.,Aoki, M.,Sekine, S.I.
Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex.
Nat Commun, 15:7854-7854, 2024

PubMed Abstract: The 5´-3´ exoribonuclease Rat1/Xrn2 is responsible for the termination of eukaryotic mRNA transcription by RNAPII. Rat1 forms a complex with its partner proteins, Rai1 and Rtt103, and acts as a "torpedo" to bind transcribing RNAPII and dissociate DNA/RNA from it. Here we report the cryo-electron microscopy structures of the Rat1-Rai1-Rtt103 complex and three Rat1-Rai1-associated RNAPII complexes (type-1, type-1b, and type-2) from the yeast, Komagataella phaffii. The Rat1-Rai1-Rtt103 structure revealed that Rat1 and Rai1 form a heterotetramer with a single Rtt103 bound between two Rai1 molecules. In the type-1 complex, Rat1-Rai1 forms a heterodimer and binds to the RNA exit site of RNAPII to extract RNA into the Rat1 exonuclease active site. This interaction changes the RNA path in favor of termination (the "pre-termination" state). The type-1b and type-2 complexes have no bound DNA/RNA, likely representing the "post-termination" states. These structures illustrate the termination mechanism of eukaryotic mRNA transcription.

PubMed: 39245712
DOI: 10.1038/s41467-024-52157-0

Experimental method

ELECTRON MICROSCOPY (3.4 Å)