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- PDB-7qdz: 80S-bound human SKI complex in the closed state -

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Basic information

Entry
Database: PDB / ID: 7qdz
Title80S-bound human SKI complex in the closed state
Components
  • Helicase SKI2W
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
  • Tetratricopeptide repeat protein 37
  • WD repeat-containing protein 61
KeywordsRNA BINDING PROTEIN / multiprotein complex / RNA helicase / DExH-box helicase / ATPase / RNA binding
Function / homology
Function and homology information


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 / Association of TriC/CCT with target proteins during biosynthesis / nuclear-transcribed mRNA catabolic process / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex ...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 / Association of TriC/CCT with target proteins during biosynthesis / nuclear-transcribed mRNA catabolic process / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / rescue of stalled ribosome / transcription elongation by RNA polymerase II / euchromatin / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ski3/TTC37 / 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 ...Ski3/TTC37 / 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 / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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
RNA / Superkiller complex protein 2 / Superkiller complex protein 3 / Superkiller complex protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKoegel, A. / Keidel, A. / Bonneau, F. / Schaefer, I.B. / Conti, E.
Funding support Germany, 5items
OrganizationGrant numberCountry
European Research Council (ERC)EXORICO Germany
German Research Foundation (DFG)DFG SFB1035 Germany
German Research Foundation (DFG)GRK1721 Germany
German Research Foundation (DFG)SFB/TRR 237 Germany
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2022
Title: The human SKI complex regulates channeling of ribosome-bound RNA to the exosome via an intrinsic gatekeeping mechanism.
Authors: Alexander Kögel / Achim Keidel / Fabien Bonneau / Ingmar B Schäfer / Elena Conti /
Abstract: The superkiller (SKI) complex is the cytoplasmic co-factor and regulator of the RNA-degrading exosome. In human cells, the SKI complex functions mainly in co-translational surveillance-decay ...The superkiller (SKI) complex is the cytoplasmic co-factor and regulator of the RNA-degrading exosome. In human cells, the SKI complex functions mainly in co-translational surveillance-decay pathways, and its malfunction is linked to a severe congenital disorder, the trichohepatoenteric syndrome. To obtain insights into the molecular mechanisms regulating the human SKI (hSKI) complex, we structurally characterized several of its functional states in the context of 80S ribosomes and substrate RNA. In a prehydrolytic ATP form, the hSKI complex exhibits a closed conformation with an inherent gating system that effectively traps the 80S-bound RNA into the hSKI2 helicase subunit. When active, hSKI switches to an open conformation in which the gating is released and the RNA 3' end exits the helicase. The emerging picture is that the gatekeeping mechanism and architectural remodeling of hSKI underpin a regulated RNA channeling system that is mechanistically conserved among the cytoplasmic and nuclear helicase-exosome complexes.
History
DepositionDec 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 2, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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  • EMDB-13928
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Assembly

Deposited unit
A: Helicase SKI2W
B: Tetratricopeptide repeat protein 37
C: WD repeat-containing protein 61
D: WD repeat-containing protein 61
E: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)385,5925
Polymers385,5925
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26380 Å2
ΔGint-153 kcal/mol
Surface area125890 Å2
MethodPISA

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Components

#1: 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 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q15477, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Tetratricopeptide repeat protein 37 / TPR repeat protein 37 / SKI3 homolog / Ski3 / Tricho-hepatic-enteric syndrome protein / Thespin


Mass: 178651.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTC37, KIAA0372 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PGP7
#3: 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 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9GZS3
#4: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: H.s. SKI complex bound to the ribosome in closed state
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.38 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf21 / Plasmid: pACEBac1
Buffer solutionpH: 7.5
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid 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 recordingAverage exposure time: 5 sec. / Electron dose: 55.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
4Gctf1.06CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51048 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL / Target criteria: CORRELATION COEFFICIENT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00723060
ELECTRON MICROSCOPYf_angle_d0.96731320
ELECTRON MICROSCOPYf_dihedral_angle_d17.9313201
ELECTRON MICROSCOPYf_chiral_restr0.0533590
ELECTRON MICROSCOPYf_plane_restr0.0074009

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