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- EMDB-3369: Cryo-EM structure of yeast cytoplasmic exosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3369
TitleCryo-EM structure of yeast cytoplasmic exosome
Map dataReconstruction of RNA-bound Exo10-Ski7 complex
Sample
  • Sample: Exosome-Ski7-RNA complex
  • Protein or peptide: Exosome-Ski7 complex
KeywordsRNA decay / Exosome / RNA quality control
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsLiu 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
CitationJournal: Cell Res / Year: 2016
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
DepositionMar 8, 2016-
Header (metadata) releaseApr 13, 2016-
Map releaseJun 15, 2016-
UpdateJul 20, 2016-
Current statusJul 20, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3369.png

Downloads & links

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Map

FileDownload / File: emd_3369.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of RNA-bound Exo10-Ski7 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 180 pix.
= 235.177 Å		1.31 Å/pix.
x 180 pix.
= 235.177 Å		1.31 Å/pix.
x 180 pix.
= 235.177 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.09354669 - 0.16752727
Average (Standard dev.)0.00102354 (±0.00826324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 235.1772 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.30653888888891.30653888888891.3065388888889
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z235.177235.177235.177
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0940.1680.001

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Supplemental data

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Sample components

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Entire : Exosome-Ski7-RNA complex

EntireName: Exosome-Ski7-RNA complex
Components
  • Sample: Exosome-Ski7-RNA complex
  • Protein or peptide: Exosome-Ski7 complex

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Supramolecule #1000: Exosome-Ski7-RNA complex

SupramoleculeName: Exosome-Ski7-RNA complex / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 420 KDa / Theoretical: 420 KDa / Method: SDS-PAG

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Macromolecule #1: Exosome-Ski7 complex

MacromoleculeName: Exosome-Ski7 complex / type: protein_or_peptide / ID: 1 / Name.synonym: PM/Scl-Ski7 complex / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast
Molecular weightExperimental: 420 KDa / Theoretical: 420 KDa

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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

Concentration2.0 mg/mL
BufferpH: 8 / Details: 150mM NaCl, 50mM Tris-HCL, 1mM DTT, 1mM EGTA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJan 3, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Ctffind3
Final reconstructionApplied 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

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