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- PDB-8qcf: yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate -

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Basic information

Entry
Database: PDB / ID: 8qcf
Titleyeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate
Components
  • (Exosome complex component ...) x 8
  • Antiviral helicase SKI2
  • Exosome complex exonuclease DIS3
  • RNA (5'hairpin 60U)
  • RRP46 isoform 1
  • Superkiller protein 7
KeywordsHYDROLASE / Helicase / RNA binding / RNA degradation
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
: / Ski2, beta-barrel domain / Ski2, N-terminal domain / : / Ski2 N-terminal region / 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 ...: / Ski2, beta-barrel domain / Ski2, N-terminal domain / : / Ski2 N-terminal region / 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 / RRP4, S1 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 / PIN domain / : / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / 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 / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / 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 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RRP46 isoform 1 / Exosome complex component RRP43 / Antiviral helicase SKI2 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component CSL4 ...ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RRP46 isoform 1 / Exosome complex component RRP43 / Antiviral helicase SKI2 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsKeidel, A. / Koegel, A. / Reichelt, P. / Kowalinski, E. / Schaefer, I.B. / Conti, E.
Funding support Germany, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Exosome complex component RRP45
C: Exosome complex component SKI6
D: Exosome complex component RRP43
E: RRP46 isoform 1
F: Exosome complex component RRP42
G: Exosome complex component MTR3
H: Exosome complex component RRP40
I: Exosome complex component RRP4
J: Exosome complex component CSL4
K: Exosome complex exonuclease DIS3
L: Superkiller protein 7
M: Antiviral helicase SKI2
N: RNA (5'hairpin 60U)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)581,98114
Polymers581,47413
Non-polymers5071
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Exosome complex component ... , 8 types, 8 molecules BCDFGHIJ

#1: Protein Exosome complex component RRP45 /


Mass: 34001.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP45 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05636
#2: Protein Exosome complex component SKI6 /


Mass: 27892.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI6 / Production host: Escherichia coli (E. coli) / References: UniProt: P46948
#3: Protein Exosome complex component RRP43 /


Mass: 44109.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP43 / Production host: Escherichia coli (E. coli) / References: UniProt: P25359
#5: Protein Exosome complex component RRP42 /


Mass: 29391.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP42 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12277
#6: Protein Exosome complex component MTR3 /


Mass: 27573.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MTR3 / Production host: Escherichia coli (E. coli) / References: UniProt: P48240
#7: Protein Exosome complex component RRP40 /


Mass: 26939.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08285
#8: Protein Exosome complex component RRP4 / / Ribosomal RNA-processing protein 4


Mass: 39929.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP4, YHR069C / Production host: Escherichia coli (E. coli) / References: UniProt: P38792
#9: Protein Exosome complex component CSL4 /


Mass: 31911.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CSL4 / Production host: Escherichia coli (E. coli) / References: UniProt: P53859

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Protein , 4 types, 4 molecules EKLM

#4: Protein RRP46 isoform 1


Mass: 24659.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRP46 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PYM9
#10: Protein Exosome complex exonuclease DIS3


Mass: 114214.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DIS3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08162
#11: Protein Superkiller protein 7


Mass: 39242.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI7, YOR076C, YOR29-27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08491
#12: Protein Antiviral helicase SKI2 / Superkiller protein 2


Mass: 117412.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SKI2, YLR398C, L8084.17 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35207, RNA helicase

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RNA chain / Non-polymers , 2 types, 2 molecules N

#13: RNA chain RNA (5'hairpin 60U)


Mass: 24196.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#14: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate
Type: COMPLEX / Entity ID: #1-#13 / Source: MULTIPLE SOURCES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 63.36 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 338757 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00331349
ELECTRON MICROSCOPYf_angle_d0.52942605
ELECTRON MICROSCOPYf_dihedral_angle_d7.8584584
ELECTRON MICROSCOPYf_chiral_restr0.0455031
ELECTRON MICROSCOPYf_plane_restr0.0055395

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