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- PDB-8q9t: CryoEM structure of a S. Cerevisiae Ski238 complex bound to RNA -

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Basic information

Entry
Database: PDB / ID: 8q9t
TitleCryoEM structure of a S. Cerevisiae Ski238 complex bound to RNA
Components
  • Antiviral helicase SKI2
  • Antiviral protein SKI8Antiviral drug
  • RNA (5'-R(P*UP*UP*UP*U)-3')
  • Superkiller protein 3
KeywordsHYDROLASE / Helicase / RNA binding / RNA degradation
Function / homology
Function and homology information


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 / reciprocal meiotic recombination / nuclear chromosome / mRNA catabolic process / regulation of translation ...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 / reciprocal meiotic recombination / nuclear chromosome / mRNA catabolic process / regulation of translation / protein-containing complex assembly / defense response to virus / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / 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 / 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
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 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)408,2455
Polymers408,2455
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


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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35207
#2: 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
#3: 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
#4: 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: Ski238 polyU RNA / Type: COMPLEX / Entity ID: #1, #3, #2, #4 / Source: MULTIPLE SOURCES
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
Specimen supportGrid type: Quantifoil R2/1
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: 67.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9416

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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: 385414 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221328
ELECTRON MICROSCOPYf_angle_d0.48729034
ELECTRON MICROSCOPYf_dihedral_angle_d4.2932975
ELECTRON MICROSCOPYf_chiral_restr0.0393410
ELECTRON MICROSCOPYf_plane_restr0.0033688

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