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- EMDB-3366: Cryo-EM structure of yeast cytoplasmic exosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3366
TitleCryo-EM structure of yeast cytoplasmic exosome
Map dataReconstruction of RNA-free Exo10-Ski7
Sample
  • Sample: Exosome-Ski7 complex
  • Protein or peptide: Exossome-SKi7 complex
KeywordsRNA decay / Exosome / RNA quality control
Function / homology
Function and homology information


Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent mRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent mRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / 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) / rRNA catabolic process / nuclear mRNA surveillance / mRNA 3'-UTR AU-rich region binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nonfunctional rRNA decay / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / translational elongation / translation elongation factor activity / RNA processing / RNA endonuclease activity / protein catabolic process / mRNA processing / manganese ion binding / protein-macromolecule adaptor activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / endonuclease activity / tRNA binding / translation / GTPase activity / protein-containing complex binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Ski7 III domain / Ski7 domain II / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain ...: / : / Ski7 III domain / Ski7 domain II / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / PIN domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / : / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / : / Large family of predicted nucleotide-binding domains / PIN domain / K Homology domain, type 1 / K Homology domain, type 1 superfamily / PIN-like domain superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / Superkiller protein 7 / Exosome complex component RRP42
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 4.2 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 1, 2016-
UpdateJul 13, 2016-
Current statusJul 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5g06
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3366.png

Downloads & links

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Map

FileDownload / File: emd_3366.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of RNA-free Exo10-Ski7
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: 0.025
Minimum - Maximum-0.0503485 - 0.11162354
Average (Standard dev.)0.00110654 (±0.0061763)
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-0.0500.1120.001

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Supplemental data

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Sample components

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Entire : Exosome-Ski7 complex

EntireName: Exosome-Ski7 complex
Components
  • Sample: Exosome-Ski7 complex
  • Protein or peptide: Exossome-SKi7 complex

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Supramolecule #1000: Exosome-Ski7 complex

SupramoleculeName: Exosome-Ski7 complex / type: sample / ID: 1000 / Details: The sample was purified from yeast with TAP tag / Number unique components: 1
Molecular weightExperimental: 420 KDa / Theoretical: 420 KDa / Method: SDS PAGE

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Macromolecule #1: Exossome-SKi7 complex

MacromoleculeName: Exossome-SKi7 complex / type: protein_or_peptide / ID: 1 / Name.synonym: PM/Scl-Ski7 complex / Oligomeric state: 11 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Location in cell: cytoplasm
Molecular weightExperimental: 420 KDa / Theoretical: 420 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo 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
StainingType: NEGATIVE / Details: Cryo Sample
GridDetails: 300 mesh 1.2/1.13 Cu grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1.5 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateOct 20, 2014
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 / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500
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: 4.2 Å / Resolution method: OTHER / Software - Name: EMAN2, IMAGIC, Relion-1.3 / Number images used: 25000

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