8QCA

CryoEM structure of a S. Cerevisiae Ski2387 complex in the closed state bound to RNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Concerted structural rearrangements enable RNA channeling into the cytoplasmic Ski238-Ski7-exosome assembly.

Keidel, A.Kogel, A.Reichelt, P.Kowalinski, E.Schafer, I.B.Conti, E.

(2023) Mol Cell 83: 4093

  • DOI: https://doi.org/10.1016/j.molcel.2023.09.037
  • Primary Citation of Related Structures:  
    8Q9T, 8QCA, 8QCB, 8QCF

  • PubMed Abstract: 

    The Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the adaptor protein Ski7. We determined different cryo-EM structures of the Ski238 complex depicting the transition from a rigid autoinhibited closed conformation to a flexible active open conformation in which the Ski2 helicase module has detached from the rest of Ski238. The open conformation favors the interaction of the Ski3 subunit with exosome-bound Ski7, leading to the recruitment of the exosome. In the Ski238-Ski7-exosome holocomplex, the Ski2 helicase module binds the exosome cap, enabling the RNA to traverse from the helicase through the internal exosome channel to the Rrp44 exoribonuclease. Our study pinpoints how conformational changes within the Ski238 complex regulate exosome recruitment for RNA degradation. We also reveal the remarkable conservation of helicase-exosome RNA channeling mechanisms throughout eukaryotic nuclear and cytoplasmic exosome complexes.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antiviral helicase SKI21,287Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKI2YLR398CL8084.17
EC: 3.6.4.13
UniProt
Find proteins for P35207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35207 
Go to UniProtKB:  P35207
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UniProt GroupP35207
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Superkiller protein 31,436Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKI3
UniProt
Find proteins for P17883 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P17883
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UniProt GroupP17883
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antiviral protein SKI8
C, D
397Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKI8
UniProt
Find proteins for Q02793 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q02793
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UniProt GroupQ02793
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Superkiller protein 7250Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKI7YOR076CYOR29-27
UniProt
Find proteins for Q08491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08491 
Go to UniProtKB:  Q08491
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UniProt GroupQ08491
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*UP*UP*U)-3')F [auth X]30Saccharomyces cerevisiae
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Database references