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Yorodumi- EMDB-18329: yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18329 | |||||||||
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Title | yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate | |||||||||
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Sample |
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Keywords | Helicase / RNA binding / RNA degradation / HYDROLASE | |||||||||
Function / homology | Function and homology information Eukaryotic Translation Elongation / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Ski complex / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing ...Eukaryotic Translation Elongation / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Ski complex / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / HSF1 activation / rRNA catabolic process / nuclear mRNA surveillance / nonfunctional rRNA decay / Protein methylation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / translational elongation / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / RNA processing / translation elongation factor activity / RNA endonuclease activity / Neutrophil degranulation / protein catabolic process / mRNA processing / protein-macromolecule adaptor activity / regulation of translation / manganese ion binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / defense response to virus / endonuclease activity / tRNA binding / RNA helicase activity / RNA helicase / translation / mRNA binding / GTPase activity / protein-containing complex binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.55 Å | |||||||||
Authors | Keidel A / Koegel A / Reichelt P / Kowalinski E / Schaefer IB / Conti E | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18329.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-18329-v30.xml emd-18329.xml | 35 KB 35 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18329_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_18329.png | 49.4 KB | ||
Masks | emd_18329_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-18329.cif.gz | 9.7 KB | ||
Others | emd_18329_additional_1.map.gz emd_18329_additional_2.map.gz emd_18329_half_map_1.map.gz emd_18329_half_map_2.map.gz | 157.8 MB 88.2 MB 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18329 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18329 | HTTPS FTP |
-Related structure data
Related structure data | 8qcfMC 8q9tC 8qcaC 8qcbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18329.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8512 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18329_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: map sharpened with deepEMhancer software (tightTarget)
File | emd_18329_additional_1.map | ||||||||||||
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Annotation | map sharpened with deepEMhancer software (tightTarget) | ||||||||||||
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Density Histograms |
-Additional map: map used to trace the flexible RNA backbone
File | emd_18329_additional_2.map | ||||||||||||
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Annotation | map used to trace the flexible RNA backbone | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_18329_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_18329_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate
+Supramolecule #1: yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate
+Macromolecule #1: Exosome complex component RRP45
+Macromolecule #2: Exosome complex component SKI6
+Macromolecule #3: Exosome complex component RRP43
+Macromolecule #4: RRP46 isoform 1
+Macromolecule #5: Exosome complex component RRP42
+Macromolecule #6: Exosome complex component MTR3
+Macromolecule #7: Exosome complex component RRP40
+Macromolecule #8: Exosome complex component RRP4
+Macromolecule #9: Exosome complex component CSL4
+Macromolecule #10: Exosome complex exonuclease DIS3
+Macromolecule #11: Superkiller protein 7
+Macromolecule #12: Antiviral helicase SKI2
+Macromolecule #13: RNA (5'hairpin 60U)
+Macromolecule #14: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.36 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |