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- EMDB-51139: human 80S ribosome bound by a SKI2-exosome complex (60S signal su... -

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Entry
Database: EMDB / ID: EMD-51139
Titlehuman 80S ribosome bound by a SKI2-exosome complex (60S signal subtracted)
Map data
Sample
  • Complex: human 80S ribosome bound by a SKI2-exosome complex (60S signal subtracted)
KeywordsRNA-binding / RNA-degradation / cytoplasm / helicase / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKoegel A / Keidel A / Loukeri MJ / Kuhn CC / Langer LM / Schaefer IB / Conti E
Funding support Germany, European Union, Denmark, 5 items
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 24, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51139.png

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Map

FileDownload / File: emd_51139.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 832 pix.
= 708.198 Å		0.85 Å/pix.
x 832 pix.
= 708.198 Å		0.85 Å/pix.
x 832 pix.
= 708.198 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.017948098 - 0.059083357
Average (Standard dev.)0.00008425216 (±0.0011025948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions832832832
Spacing832832832
CellA=B=C: 708.19836 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51139_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_51139_half_map_1.map
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Half map: #2

Fileemd_51139_half_map_2.map
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Sample components

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Entire : human 80S ribosome bound by a SKI2-exosome complex (60S signal su...

EntireName: human 80S ribosome bound by a SKI2-exosome complex (60S signal subtracted)
Components
  • Complex: human 80S ribosome bound by a SKI2-exosome complex (60S signal subtracted)

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Supramolecule #1: human 80S ribosome bound by a SKI2-exosome complex (60S signal su...

SupramoleculeName: human 80S ribosome bound by a SKI2-exosome complex (60S signal subtracted)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4ug0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79353
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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