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- PDB-9g8p: 40S-bound human SKI2-exosome complex -

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Basic information

Entry
Database: PDB / ID: 9g8p
Title40S-bound human SKI2-exosome complex
Components
  • (Exosome complex component ...) x 9
  • CrPV-IRES RNA
  • DIS3-like exonuclease 1
  • Helicase SKI2W
  • Isoform 2 of HBS1-like protein
KeywordsRIBOSOME / RNA-binding / RNA-degradation / cytoplasm / helicase
Function / homology
Function and homology information


DNA deamination / nucleolar exosome (RNase complex) / exoribonuclease II activity / exoribonuclease II / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / Ski complex ...DNA deamination / nucleolar exosome (RNase complex) / exoribonuclease II activity / exoribonuclease II / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / Ski complex / CUT catabolic process / exosome (RNase complex) / U4 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / histone mRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of isotype switching / 3'-5' RNA helicase activity / nuclear mRNA surveillance / rRNA catabolic process / 7S RNA binding / mRNA 3'-UTR AU-rich region binding / isotype switching / ribosome disassembly / RNA catabolic process / KSRP (KHSRP) binds and destabilizes mRNA / maturation of 5.8S rRNA / nuclear chromosome / mRNA catabolic process / Association of TriC/CCT with target proteins during biosynthesis / nuclear-transcribed mRNA catabolic process / translation elongation factor activity / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / cytosolic ribosome / rescue of stalled ribosome / euchromatin / fibrillar center / rRNA processing / chromosome / positive regulation of cell growth / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / ciliary basal body / immune response / RNA helicase / translation / GTPase activity / intracellular membrane-bounded organelle / centrosome / GTP binding / nucleolus / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / HBS1-like protein, N-terminal domain superfamily / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / Exosome complex exonuclease RRP44, S1 domain / S1 domain ...Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / HBS1-like protein, N-terminal domain superfamily / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / Exosome complex exonuclease RRP44, S1 domain / 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 / 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 / rRNA-processing arch domain / Ribonuclease II family signature. / Mtr4-like, beta-barrel domain / : / Ribonuclease II/R / RNB domain / RNB / : / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / : / GTP-eEF1A C-terminal domain-like / 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 / : / K Homology domain, type 1 / K Homology domain, type 1 superfamily / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / 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. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Superkiller complex protein 2 / Exosome complex component MTR3 / DIS3-like exonuclease 1 / Exosome complex component RRP43 / Exosome complex component RRP41 ...RNA / RNA (> 10) / Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Superkiller complex protein 2 / Exosome complex component MTR3 / DIS3-like exonuclease 1 / Exosome complex component RRP43 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 / Exosome complex component CSL4 / HBS1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Cricket paralysis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsKoegel, A. / Keidel, A. / Loukeri, M.J. / Kuhn, C.C. / Langer, L.M. / Schaefer, I.B. / Conti, E.
Funding support Germany, European Union, Denmark, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)740329European Union
European Research Council (ERC)101054447European Union
German Research Foundation (DFG)SFB1035 Germany
Novo Nordisk Foundation31199 Denmark
CitationJournal: Nature / Year: 2024
Title: Structural basis of mRNA decay by the human exosome-ribosome supercomplex.
Authors: Alexander Kögel / Achim Keidel / Matina-Jasemi Loukeri / Christopher C Kuhn / Lukas M Langer / Ingmar B Schäfer / Elena Conti /
Abstract: The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated ...The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated largely by the cytoplasmic exosome, which includes the exoribonuclease complex EXO10 and the helicase complex SKI238 (refs. ). The helicase can extract mRNA from the ribosome and is expected to transfer it to the exoribonuclease core through a bridging factor, HBS1L3 (also known as SKI7), but the mechanisms of this molecular handover remain unclear. Here we reveal how human EXO10 is recruited by HBS1L3 (SKI7) to an active ribosome-bound SKI238 complex. We show that rather than a sequential handover, a direct physical coupling mechanism takes place, which culminates in the formation of a cytoplasmic exosome-ribosome supercomplex. Capturing the structure during active decay reveals a continuous path in which an RNA substrate threads from the 80S ribosome through the SKI2 helicase into the exoribonuclease active site of the cytoplasmic exosome complex. The SKI3 subunit of the complex directly binds to HBS1L3 (SKI7) and also engages a surface of the 40S subunit, establishing a recognition platform in collided disomes. Exosome and ribosome thus work together as a single structural and functional unit in co-translational mRNA decay, coordinating their activities in a transient supercomplex.
History
DepositionJul 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Exosome complex component RRP43
O: Exosome complex component RRP46
F: Exosome complex component RRP42
H: Exosome complex component RRP40
J: Exosome complex component CSL4
X: CrPV-IRES RNA
A: Helicase SKI2W
G: Exosome complex component MTR3
I: Exosome complex component RRP4
E: Isoform 2 of HBS1-like protein
K: Exosome complex component RRP45
M: DIS3-like exonuclease 1
L: Exosome complex component RRP41


Theoretical massNumber of molelcules
Total (without water)579,94413
Polymers579,94413
Non-polymers00
Water00
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 ... , 9 types, 9 molecules NOFHJGIKL

#1: Protein Exosome complex component RRP43 / Exosome component 8 / Opa-interacting protein 2 / OIP-2 / Ribosomal RNA-processing protein 43 / p9


Mass: 30429.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC8, OIP2, RRP43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96B26
#2: Protein Exosome complex component RRP46 / Chronic myelogenous leukemia tumor antigen 28 / Exosome component 5 / Ribosomal RNA-processing ...Chronic myelogenous leukemia tumor antigen 28 / Exosome component 5 / Ribosomal RNA-processing protein 46 / p12B


Mass: 25636.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC5, CML28, RRP46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQT4
#3: Protein Exosome complex component RRP42 / Exosome component 7 / Ribosomal RNA-processing protein 42 / p8


Mass: 32216.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC7, KIAA0116, RRP42 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15024
#4: Protein Exosome complex component RRP40 / Exosome component 3 / Ribosomal RNA-processing protein 40 / p10


Mass: 29940.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC3, RRP40, CGI-102 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQT5
#5: Protein Exosome complex component CSL4 / Exosome component 1


Mass: 21835.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC1, CSL4, CGI-108 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3B2
#8: Protein Exosome complex component MTR3 / Exosome component 6 / mRNA transport regulator 3 homolog / hMtr3 / p11


Mass: 28267.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC6, MTR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RKV6
#9: Protein Exosome complex component RRP4 / Exosome component 2 / Ribosomal RNA-processing protein 4


Mass: 33190.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC2, RRP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13868
#11: Protein Exosome complex component RRP45 / Autoantigen PM/Scl 1 / Exosome component 9 / P75 polymyositis-scleroderma overlap syndrome- ...Autoantigen PM/Scl 1 / Exosome component 9 / P75 polymyositis-scleroderma overlap syndrome-associated autoantigen / Polymyositis/scleroderma autoantigen 1 / Polymyositis/scleroderma autoantigen 75 kDa / PM/Scl-75


Mass: 49370.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC9, PMSCL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06265
#13: Protein Exosome complex component RRP41 / Exosome component 4 / Ribosomal RNA-processing protein 41 / p12A


Mass: 26416.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC4, RRP41, SKI6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPD3

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RNA chain , 1 types, 1 molecules X

#6: RNA chain CrPV-IRES RNA


Mass: 13422.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cricket paralysis virus

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Protein , 3 types, 3 molecules AEM

#7: Protein Helicase SKI2W / Ski2 / Helicase-like protein / HLP


Mass: 137913.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKIV2L, DDX13, SKI2W, SKIV2, W / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q15477, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#10: Protein Isoform 2 of HBS1-like protein / ERFS


Mass: 30196.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBS1L, HBS1, KIAA1038 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y450, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#12: Protein DIS3-like exonuclease 1


Mass: 121108.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIS3L, DIS3L1, KIAA1955 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TF46, exoribonuclease II

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Details

Has protein modificationN

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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: 40S-bound human SKI2-exosome complex / Type: RIBOSOME / Entity ID: #13, #1-#12 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 200 divisions/in. / Grid 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 64.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12714 / Symmetry type: POINT

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