5G06

Cryo-EM structure of yeast cytoplasmic exosome

Summary for 5G06

• Entry DOI: 10.2210/pdb5g06/pdb
• EMDB information: 3366
• Descriptor: EXOSOME COMPLEX COMPONENT RRP45, EXOSOME COMPLEX EXONUCLEASE DIS3, SUPERKILLER PROTEIN 7, ... (11 entities in total)
• Functional Keywords: hydrolase, rna decay, exosome, rna quality control
• Biological source: SACCHAROMYCES CEREVISIAE (BAKER'S YEAST); More
• Cellular location: Cytoplasm : Q05636 Q08162 Q08491 P46948 P25359 P53256 Q12277 P48240 Q08285 P38792 P53859
• Total number of polymer chains: 11
• Total formula weight: 483231.21

Authors

Liu, J.J.,Niu, C.Y.,Wu, Y.,Tan, D.,Wang, Y.,Ye, M.D.,Liu, Y.,Zhao, W.W.,Zhou, K.,Liu, Q.S.,Dai, J.B.,Yang, X.R.,Dong, M.Q.,Huang, N.,Wang, H.W. (deposition date: 2016-03-17, release date: 2016-06-15, Last modification date: 2024-11-06)

Primary citation

Liu, J.,Niu, C.,Wu, Y.,Tan, D.,Wang, Y.,Ye, M.,Liu, Y.,Zhao, W.,Zhou, K.,Liu, Q.,Dai, J.,Yang, X.,Dong, M.,Huang, N.,Wang, H.
Cryoem Structure of Yeast Cytoplasmic Exosome Complex.
Cell Res., 26:822-, 2016

PubMed Abstract: The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing.

PubMed: 27174052
DOI: 10.1038/CR.2016.56

Experimental method

ELECTRON MICROSCOPY (4.2 Å)