4IFD

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Summary for 4IFD

• Entry DOI: 10.2210/pdb4ifd/pdb
• Descriptor: Exosome complex component RRP45, Exosome complex exonuclease DIS3, Exosome complex exonuclease RRP6, ... (18 entities in total)
• Functional Keywords: exosome, rna, rrp44, dis3, pin, rrp6, exonuclease, endonuclease, hydrolase, nuclease, ribonuclease, rna processing, hydrolase-rna complex, hydrolase/rna
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Cellular location: Cytoplasm : Q05636 Q08162 P46948 P25359 P53256 Q12277 P48240 Q08285 P38792 P53859; Nucleus, nucleolus : Q12149
• Total number of polymer chains: 12
• Total formula weight: 438162.46

Authors

Makino, D.L.,Conti, E. (deposition date: 2012-12-14, release date: 2013-02-06, Last modification date: 2024-10-30)

Primary citation

Makino, D.L.,Baumgartner, M.,Conti, E.
Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.
Nature, 495:70-75, 2013

PubMed Abstract: The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44. In the nucleus, the Exo-10 core recruits another nuclease, Rrp6. Here we crystallized an approximately 440-kilodalton complex of Saccharomyces cerevisiae Exo-10 bound to a carboxy-terminal region of Rrp6 and to an RNA duplex with a 3'-overhang of 31 ribonucleotides. The 2.8 Å resolution structure shows how RNA is funnelled into the Exo-9 channel in a single-stranded conformation by an unwinding pore. Rrp44 adopts a closed conformation and captures the RNA 3'-end that exits from the side of Exo-9. Exo-9 subunits bind RNA with sequence-unspecific interactions reminiscent of archaeal exosomes. The substrate binding and channelling mechanisms of 3'-5' RNA degradation complexes are conserved in all kingdoms of life.

PubMed: 23376952
DOI: 10.1038/nature11870

Experimental method

X-RAY DIFFRACTION (2.805 Å)