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- PDB-8qca: CryoEM structure of a S. Cerevisiae Ski2387 complex in the closed... -

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Basic information

Entry
Database: PDB / ID: 8qca
TitleCryoEM structure of a S. Cerevisiae Ski2387 complex in the closed state bound to RNA
Components
  • Antiviral helicase SKI2
  • Antiviral protein SKI8Antiviral drug
  • RNA (5'-R(P*UP*UP*UP*U)-3')
  • Superkiller protein 3
  • Superkiller protein 7
KeywordsHYDROLASE / Helicase / RNA binding / RNA degradation
Function / homology
Function and homology information


Eukaryotic Translation Elongation / Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / nonfunctional rRNA decay / Protein methylation ...Eukaryotic Translation Elongation / Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / nonfunctional rRNA decay / Protein methylation / reciprocal meiotic recombination / translational elongation / nuclear chromosome / mRNA catabolic process / translation elongation factor activity / Neutrophil degranulation / protein catabolic process / protein-macromolecule adaptor activity / regulation of translation / protein-containing complex assembly / defense response to virus / RNA helicase activity / RNA helicase / translation / mRNA binding / GTPase activity / protein-containing complex binding / GTP binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide-like repeat / Tetratricopeptide repeat / : / Ski2, beta-barrel domain / Ski3/TTC37 / Ski2, N-terminal domain / Ski2 N-terminal region / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal ...Tetratricopeptide-like repeat / Tetratricopeptide repeat / : / Ski2, beta-barrel domain / Ski3/TTC37 / Ski2, N-terminal domain / Ski2 N-terminal region / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Tetratricopeptide repeats / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Tetratricopeptide repeat / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Tetratricopeptide-like helical domain superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Superkiller protein 3 / Antiviral helicase SKI2 / Antiviral protein SKI8 / Superkiller protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsKeidel, A. / Koegel, A. / Reichelt, P. / Kowalinski, E. / Schaefer, I.B. / Conti, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2023
Title: Concerted structural rearrangements enable RNA channeling into the cytoplasmic Ski238-Ski7-exosome assembly.
Authors: Achim Keidel / Alexander Kögel / Peter Reichelt / Eva Kowalinski / Ingmar B Schäfer / Elena Conti /
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 ...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.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antiviral helicase SKI2
B: Superkiller protein 3
C: Antiviral protein SKI8
D: Antiviral protein SKI8
E: Superkiller protein 7
X: RNA (5'-R(P*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)436,5906
Polymers436,5906
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Antiviral helicase SKI2 / Superkiller protein 2


Mass: 146259.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI2, YLR398C, L8084.17 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35207, RNA helicase
#2: Protein Superkiller protein 3


Mass: 164278.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P17883
#3: Protein Antiviral protein SKI8 / Antiviral drug


Mass: 44283.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q02793
#4: Protein Superkiller protein 7


Mass: 28345.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI7, YOR076C, YOR29-27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08491
#5: RNA chain RNA (5'-R(P*UP*UP*UP*U)-3')


Mass: 9140.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ski2delarch387 PolyU RNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 77.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7127

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Processing

EM softwareName: cryoSPARC / Version: 3.3.2 / Category: classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 371916 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418039
ELECTRON MICROSCOPYf_angle_d0.54424547
ELECTRON MICROSCOPYf_dihedral_angle_d4.4832528
ELECTRON MICROSCOPYf_chiral_restr0.0432864
ELECTRON MICROSCOPYf_plane_restr0.0043133

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