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- PDB-9g8r: human SKI7-SKI238 complex in the open state -

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Basic information

Entry
Database: PDB / ID: 9g8r
Titlehuman SKI7-SKI238 complex in the open state
Components
  • Isoform 2 of HBS1-like protein
  • Superkiller complex protein 2
  • Superkiller complex protein 3
  • WD repeat-containing protein 61
KeywordsHYDROLASE / Helicase / RNA-binding / RNA-degradation / cytoplasm
Function / homology
Function and homology information


Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / Ski complex / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / 3'-5' RNA helicase activity / ribosome disassembly / Association of TriC/CCT with target proteins during biosynthesis ...Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / Ski complex / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / 3'-5' RNA helicase activity / ribosome disassembly / Association of TriC/CCT with target proteins during biosynthesis / nuclear-transcribed mRNA catabolic process / translation elongation factor activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / cytosolic ribosome / rescue of stalled ribosome / transcription elongation by RNA polymerase II / euchromatin / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / RNA helicase activity / RNA helicase / translation / GTPase activity / GTP binding / signal transduction / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
HBS1-like protein, N-terminal domain superfamily / Ski3/TTC37 / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / : / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal ...HBS1-like protein, N-terminal domain superfamily / Ski3/TTC37 / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / : / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / 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 / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tetratricopeptide repeat / Translation elongation factor EFTu-like, domain 2 / TPR repeat region circular profile. / Elongation factor Tu domain 2 / TPR repeat profile. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Tetratricopeptide repeats / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Tetratricopeptide repeat / Helicase conserved C-terminal domain / Tetratricopeptide-like helical domain superfamily / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Superkiller complex protein 2 / Superkiller complex protein 3 / Superkiller complex protein 8 / HBS1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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
B: Superkiller complex protein 3
C: WD repeat-containing protein 61
D: WD repeat-containing protein 61
E: Isoform 2 of HBS1-like protein
A: Superkiller complex protein 2


Theoretical massNumber of molelcules
Total (without water)370,2515
Polymers370,2515
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

#1: Protein Superkiller complex protein 3 / Ski3 / Tetratricopeptide repeat protein 37 / TPR repeat protein 37 / Tricho-hepatic-enteric ...Ski3 / Tetratricopeptide repeat protein 37 / TPR repeat protein 37 / Tricho-hepatic-enteric syndrome protein / Thespin


Mass: 176064.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKIC3, KIAA0372, TTC37 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PGP7
#2: Protein WD repeat-containing protein 61 / Meiotic recombination REC14 protein homolog / SKI8 homolog / Ski8


Mass: 33617.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR61 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9GZS3
#3: Protein Isoform 2 of HBS1-like protein / ERFS


Mass: 19333.492 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
#4: Protein Superkiller complex protein 2 / Ski2 / Helicase-like protein / HLP


Mass: 107617.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKIC2, DDX13, SKI2W, SKIV2, SKIV2L, W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15477, RNA helicase
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: human SKI7-SKI238 complex in the open state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
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: FEI TITAN 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: 67.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151860 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 69.26 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003215152
ELECTRON MICROSCOPYf_angle_d0.837920564
ELECTRON MICROSCOPYf_chiral_restr0.04622322
ELECTRON MICROSCOPYf_plane_restr0.00652616
ELECTRON MICROSCOPYf_dihedral_angle_d14.71995482

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