5C0X image
Entry Detail
PDB ID:
5C0X
Keywords:
Title:
Structure of a 12-subunit nuclear exosome complex bound to structured RNA
Biological Source:
PDB Version:
Deposition Date:
2015-06-12
Release Date:
2015-08-05
Method Details:
Experimental Method:
Resolution:
3.81 Å
R-Value Free:
0.29
R-Value Work:
0.29
R-Value Observed:
0.29
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Exosome complex component RRP45
Chain IDs:A
Chain Length:305
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex component SKI6
Chain IDs:B
Chain Length:248
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex component RRP43
Chain IDs:C
Chain Length:394
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex component RRP46
Chain IDs:D
Chain Length:245
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex component RRP42
Mutations:V138I
Chain IDs:E
Chain Length:267
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex component MTR3
Mutations:T75S, M161T
Chain IDs:F
Chain Length:250
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex component RRP40
Chain IDs:G
Chain Length:243
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex component RRP4
Chain IDs:H
Chain Length:361
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex component CSL4
Chain IDs:I
Chain Length:295
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex exonuclease DIS3
Mutations:D171N, D551N
Chain IDs:J
Chain Length:1003
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Description:Exosome complex exonuclease RRP6
Mutations:D296N
Chain IDs:K
Chain Length:695
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Description:RNA synthetic
Chain IDs:L (auth: R)
Chain Length:45
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
RNA degradation paths in a 12-subunit nuclear exosome complex.
Nature 524 54 58 (2015)
PMID: 26222026 DOI: 10.1038/nature14865

Abstact

The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we report the crystal structures of a yeast nuclear exosome containing the 9-subunit core, the 3'-5' RNases Rrp44 and Rrp6, and the obligate Rrp6-binding partner Rrp47 in complex with different RNAs. The combined structural and biochemical data of this 12-subunit complex reveal how a single-stranded RNA can reach the Rrp44 or Rrp6 active sites directly or can bind Rrp6 and be threaded via the central channel towards the distal RNase Rrp44. When a bulky RNA is stalled at the entrance of the channel, Rrp6-Rrp47 swings open. The results suggest how the same molecular machine can coordinate processive degradation and partial trimming in an RNA-dependent manner by a concerted swinging mechanism of the two RNase subunits.

Legend

Protein

Chemical

Disease

Primary Citation of related structures