5G06

Cryo-EM structure of yeast cytoplasmic exosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 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

  • 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 targe ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT RRP45
A
305Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP45
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05636
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT SKI6
B
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKI6 (ECM20, RRP41)
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46948
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT RRP43
C
394Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP43
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25359
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT RRP46
D
223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP46
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53256
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT RRP42
E
265Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP42
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12277
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT MTR3
F
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MTR3
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P48240
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT RRP40
G
240Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP40
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08285
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT RRP4
H
359Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP4
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38792
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX COMPONENT CSL4
I
292Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CSL4 (SKI4)
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53859
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
EXOSOME COMPLEX EXONUCLEASE DIS3
J
1001Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DIS3 (RRP44)
EC: 3.1.13.-, 3.1.26.-
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: DIS3
Go to UniProtKB:  Q08162
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
SUPERKILLER PROTEIN 7
P
747Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKI7
Find proteins for Q08491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08491
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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