Journal: 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
Deposition
Dec 1, 2021
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Header (metadata) release
Feb 9, 2022
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Map release
Feb 9, 2022
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Update
Jul 17, 2024
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Current status
Jul 17, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Entire : H.s. SKI complex bound to the ribosome in open state
Entire
Name: H.s. SKI complex bound to the ribosome in open state
Components
Complex: H.s. SKI complex bound to the ribosome in open state
Protein or peptide: Helicase SKI2W
RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
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Supramolecule #1: H.s. SKI complex bound to the ribosome in open state
Supramolecule
Name: H.s. SKI complex bound to the ribosome in open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)
Organism: Homo sapiens (human)
Molecular weight
Theoretical: 380 KDa
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Macromolecule #1: Helicase SKI2W
Macromolecule
Name: Helicase SKI2W / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Name: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)
Organism: Homo sapiens (human)
Molecular weight
Theoretical: 2.710535 KDa
Sequence
String:
UUUUUUUUU
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
0.2 mg/mL
Buffer
pH: 7.5
Grid
Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
Vitrification
Cryogen name: ETHANE-PROPANE
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 6.0 sec. / Average electron dose: 67.62 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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