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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3369 | |||||||||
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Title | Cryo-EM structure of yeast cytoplasmic exosome | |||||||||
![]() | Reconstruction of RNA-bound Exo10-Ski7 complex | |||||||||
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![]() | RNA decay / Exosome / RNA quality control | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
![]() | Liu JJ / Niu CY / Wu Y / Tan D / Wang Y / Ye MD / Liu Y / Zhao WW / Zhou K / Liu QS ...Liu JJ / Niu CY / Wu Y / Tan D / Wang Y / Ye MD / Liu Y / Zhao WW / Zhou K / Liu QS / Dai JB / Yang XR / Dong MQ / Huang N / Wang HW | |||||||||
![]() | ![]() Title: CryoEM structure of yeast cytoplasmic exosome complex. Authors: Jun-Jie Liu / Chu-Ya Niu / Yao Wu / Dan Tan / Yang Wang / Ming-Da Ye / Yang Liu / Wenwei Zhao / Ke Zhou / Quan-Sheng Liu / Junbiao Dai / Xuerui Yang / Meng-Qiu Dong / Niu Huang / Hong-Wei Wang / ![]() Abstract: The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. ...The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.2 KB 8.2 KB | Display Display | ![]() |
Images | ![]() | 147 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3366C ![]() 3367C ![]() 3368C ![]() 3370C ![]() 3371C ![]() 3372C ![]() 5g06C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of RNA-bound Exo10-Ski7 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.30654 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Exosome-Ski7-RNA complex
Entire | Name: Exosome-Ski7-RNA complex |
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Components |
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-Supramolecule #1000: Exosome-Ski7-RNA complex
Supramolecule | Name: Exosome-Ski7-RNA complex / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 420 KDa / Theoretical: 420 KDa / Method: SDS-PAG |
-Macromolecule #1: Exosome-Ski7 complex
Macromolecule | Name: Exosome-Ski7 complex / type: protein_or_peptide / ID: 1 / Name.synonym: PM/Scl-Ski7 complex / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 420 KDa / Theoretical: 420 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 8 / Details: 150mM NaCl, 50mM Tris-HCL, 1mM DTT, 1mM EGTA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jan 3, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 21 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Ctffind3 |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: OTHER / Software - Name: EMAN2, IMAGIC, Relion-1.3 / Number images used: 35000 |