Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 11-mer - A1B1C1D1E1F1G1H1I1J1K1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 11-mer - A4B1C1D1E1F1G1H1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 483.23 kDa 
• Atom Count: 26794 
• Modelled Residue Count: 3420 
• Deposited Residue Count: 4322 
• Unique protein chains: 11

5G06

Cryo-EM structure of yeast cytoplasmic exosome

• DOI: 10.2210/pdb5G06/pdb
• EMDataResource: EMD-3366

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2016-03-17 Released: 2016-06-15 
• Deposition Author(s): Liu, J.J., Niu, C.Y., Wu, Y., Tan, D., Wang, Y., Ye, M.D., Liu, Y., Zhao, W.W., Zhou, K., Liu, Q.S., Dai, J.B., Yang, X.R., Dong, M.Q., Huang, N., Wang, H.W.

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Experimental Data Snapshot

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

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

• PubMed: 27174052 
• 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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT RRP45	A	305	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05636  Go to UniProtKB:  Q05636

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT SKI6	B	246	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46948  Go to UniProtKB:  P46948

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT RRP43	C	394	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25359  Go to UniProtKB:  P25359

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT RRP46	D	223	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53256  Go to UniProtKB:  P53256

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT RRP42	E	265	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12277  Go to UniProtKB:  Q12277

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT MTR3	F	250	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48240  Go to UniProtKB:  P48240

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT RRP40	G	240	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08285  Go to UniProtKB:  Q08285

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT RRP4	H	359	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38792  Go to UniProtKB:  P38792

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX COMPONENT CSL4	I	292	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53859  Go to UniProtKB:  P53859

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOSOME COMPLEX EXONUCLEASE DIS3	J	1001	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.1.13.1 (PDB Primary Data), 3.1.13 (UniProt), 3.1.26 (UniProt)
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08162  Go to UniProtKB:  Q08162

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
SUPERKILLER PROTEIN 7	P	747	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for Q08491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08491  Go to UniProtKB:  Q08491

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-17 
• Released Date: 2016-06-15 
Deposition Author(s): Liu, J.J., Niu, C.Y., Wu, Y., Tan, D., Wang, Y., Ye, M.D., Liu, Y., Zhao, W.W., Zhou, K., Liu, Q.S., Dai, J.B., Yang, X.R., Dong, M.Q., Huang, N., Wang, H.W.

Revision History  

• 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