5K36

Structure of an eleven component nuclear RNA exosome complex bound to RNA

Summary for 5K36

• Entry DOI: 10.2210/pdb5k36/pdb
• Descriptor: Exosome complex component RRP45, Exosome complex exonuclease RRP6, Exosome complex exonuclease DIS3, ... (16 entities in total)
• Functional Keywords: exoribonuclease, complex, rna, structural protein, hydrolase-rna complex, hydrolase/rna
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 13
• Total formula weight: 477520.40

Authors

Lima, C.D.,Zinder, J.C. (deposition date: 2016-05-19, release date: 2016-11-02, Last modification date: 2023-09-27)

Primary citation

Zinder, J.C.,Wasmuth, E.V.,Lima, C.D.
Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3.
Mol.Cell, 64:734-745, 2016

PubMed Abstract: The eukaryotic RNA exosome is an essential and conserved 3'-to-5' exoribonuclease complex that degrades or processes nearly every class of cellular RNA. The nuclear RNA exosome includes a 9-subunit non-catalytic core that binds Rrp44 (Dis3) and Rrp6 subunits to modulate their processive and distributive 3'-to-5' exoribonuclease activities, respectively. Here we utilize an engineered RNA with two 3' ends to obtain a crystal structure of an 11-subunit nuclear exosome bound to RNA at 3.1 Å. The structure reveals an extended RNA path to Rrp6 that penetrates into the non-catalytic core; contacts between the non-catalytic core and Rrp44, which inhibit exoribonuclease activity; and features of the Rrp44 exoribonuclease site that support its ability to degrade 3' phosphate RNA substrates. Using reconstituted exosome complexes, we show that 3' phosphate RNA is not a substrate for Rrp6 but is readily degraded by Rrp44 in the nuclear exosome.

PubMed: 27818140
DOI: 10.1016/j.molcel.2016.09.038

Experimental method

X-RAY DIFFRACTION (3.1 Å)