7QDR

Apo human SKI complex in the closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

The human SKI complex regulates channeling of ribosome-bound RNA to the exosome via an intrinsic gatekeeping mechanism.

Kogel, A.Keidel, A.Bonneau, F.Schafer, I.B.Conti, E.

(2022) Mol Cell 82: 756

  • DOI: https://doi.org/10.1016/j.molcel.2022.01.009
  • Primary Citation of Related Structures:  
    7QDR, 7QDS, 7QDY, 7QDZ, 7QE0

  • PubMed Abstract: 

    The superkiller (SKI) complex is the cytoplasmic co-factor and regulator of the RNA-degrading exosome. In human cells, the SKI complex functions mainly in co-translational surveillance-decay pathways, and its malfunction is linked to a severe congenital disorder, the trichohepatoenteric syndrome. To obtain insights into the molecular mechanisms regulating the human SKI (hSKI) complex, we structurally characterized several of its functional states in the context of 80S ribosomes and substrate RNA. In a prehydrolytic ATP form, the hSKI complex exhibits a closed conformation with an inherent gating system that effectively traps the 80S-bound RNA into the hSKI2 helicase subunit. When active, hSKI switches to an open conformation in which the gating is released and the RNA 3' end exits the helicase. The emerging picture is that the gatekeeping mechanism and architectural remodeling of hSKI underpin a regulated RNA channeling system that is mechanistically conserved among the cytoplasmic and nuclear helicase-exosome complexes.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase SKI2W1,246Homo sapiensMutation(s): 0 
Gene Names: SKIV2LDDX13SKI2WSKIV2W
EC: 3.6.4 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15477 (Homo sapiens)
Explore Q15477 
Go to UniProtKB:  Q15477
PHAROS:  Q15477
GTEx:  ENSG00000204351 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15477
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tetratricopeptide repeat protein 371,589Homo sapiensMutation(s): 0 
Gene Names: TTC37KIAA0372
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PGP7 (Homo sapiens)
Explore Q6PGP7 
Go to UniProtKB:  Q6PGP7
PHAROS:  Q6PGP7
GTEx:  ENSG00000198677 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PGP7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 61
C, D
305Homo sapiensMutation(s): 0 
Gene Names: WDR61
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZS3 (Homo sapiens)
Explore Q9GZS3 
Go to UniProtKB:  Q9GZS3
PHAROS:  Q9GZS3
GTEx:  ENSG00000140395 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZS3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)GermanyEXORICO
German Research Foundation (DFG)GermanyDFG SFB1035
German Research Foundation (DFG)GermanyGRK1721
German Research Foundation (DFG)GermanySFB/TRR 237
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-03-02
    Changes: Database references
  • Version 1.3: 2024-07-17
    Changes: Data collection