5G06

Cryo-EM structure of yeast cytoplasmic exosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryoem Structure of Yeast Cytoplasmic Exosome Complex.

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.

(2016) Cell Res 26: 822

  • DOI: 10.1038/cr.2016.56
  • Primary Citation of Related Structures:  
    5G06

  • 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 ...

    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.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX COMPONENT RRP45 A305Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX COMPONENT SKI6 B246Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX COMPONENT RRP43 C394Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX COMPONENT RRP46 D223Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX COMPONENT RRP42 E265Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX COMPONENT MTR3 F250Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
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EXOSOME COMPLEX COMPONENT RRP40 G240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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EXOSOME COMPLEX COMPONENT RRP4 H359Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
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EXOSOME COMPLEX COMPONENT CSL4 I292Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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EXOSOME COMPLEX EXONUCLEASE DIS3 J1001Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1.13.1 (PDB Primary Data), 3.1.13 (UniProt), 3.1.26 (UniProt)
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Entity ID: 11
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SUPERKILLER PROTEIN 7 P747Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q08491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references, Other
  • Version 1.2: 2017-04-19
    Changes: Other
  • Version 1.3: 2017-08-02
    Changes: Data collection