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- EMDB-18327: CryoEM structure of a S. Cerevisiae Ski2387 complex in an interme... -

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Basic information

Entry
Database: EMDB / ID: EMD-18327
TitleCryoEM structure of a S. Cerevisiae Ski2387 complex in an intermediate state bound to RNA
Map data
Sample
  • Complex: Ski2delarch387 PolyU RNA
KeywordsHelicase / RNA binding / RNA degradation / HYDROLASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsKeidel A / Koegel A / Reichelt P / Kowalinski E / Schaefer IB / Conti E
Funding support Germany, 1 items
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, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18327.png

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Map

FileDownload / File: emd_18327.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 352 pix.
= 299.622 Å		0.85 Å/pix.
x 352 pix.
= 299.622 Å		0.85 Å/pix.
x 352 pix.
= 299.622 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
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Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.4924903 - 3.9633484
Average (Standard dev.)-0.002363205 (±0.101209424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 299.6224 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18327_msk_1.map
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Additional map: sharpened with deepEMhancer software (tightTarget)

Fileemd_18327_additional_1.map
Annotationsharpened with deepEMhancer software (tightTarget)
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Half map: #1

Fileemd_18327_half_map_1.map
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Half map: #2

Fileemd_18327_half_map_2.map
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Sample components

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Entire : Ski2delarch387 PolyU RNA

EntireName: Ski2delarch387 PolyU RNA
Components
  • Complex: Ski2delarch387 PolyU RNA

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Supramolecule #1: Ski2delarch387 PolyU RNA

SupramoleculeName: Ski2delarch387 PolyU RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 9416 / Average electron dose: 67.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104956
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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