8QCF

yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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: 4093-4105.e7

  • 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
Exosome complex component RRP45A [auth B]305Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRP45
UniProt
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UniProt GroupQ05636
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component SKI6B [auth C]249Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKI6
UniProt
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP46948
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP43C [auth D]394Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRP43
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RRP46 isoform 1D [auth E]226Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRP46
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP42E [auth F]268Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRP42
UniProt
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UniProt GroupQ12277
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component MTR3F [auth G]250Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MTR3
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP40G [auth H]244Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRP40
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP4H [auth I]364Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRP4YHR069C
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component CSL4I [auth J]295Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CSL4
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS3J [auth K]1,005Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DIS3
EC: 3.1.13 (UniProt), 3.1.26 (UniProt)
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Superkiller protein 7K [auth L]353Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKI7YOR076CYOR29-27
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Antiviral helicase SKI2L [auth M]1,040Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKI2YLR398CL8084.17
EC: 3.6.4.13
UniProt
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Entity ID: 13
MoleculeChains LengthOrganismImage
RNA (5'hairpin 60U)M [auth N]78Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
N [auth M]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 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: 2024-01-10
    Type: Initial release