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- EMDB-16571: Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) -... -

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Basic information

Entry
Database: EMDB / ID: EMD-16571
TitleStructure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - consensus map
Map data
Sample
  • Complex: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
    • Complex: RQT complex (Slh1, Cue3 and Rqt4)
    • Complex: ribosome
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBest KM / Ikeuchi K / Kater L / Best DM / Musial J / Matsuo Y / Berninghausen O / Becker T / Inada T / Beckmann R
Funding supportEuropean Union, Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)885711European Union
German Research Foundation (DFG)BE 1814/15-1 Germany
German Research Foundation (DFG)RTG1721 Germany
Citation
Journal: Nat Commun / Year: 2023
Title: Structural basis for clearing of ribosome collisions by the RQT complex.
Authors: Katharina Best / Ken Ikeuchi / Lukas Kater / Daniel Best / Joanna Musial / Yoshitaka Matsuo / Otto Berninghausen / Thomas Becker / Toshifumi Inada / Roland Beckmann /
Abstract: Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality ...Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality control pathways. Ribosome-associated quality control facilitates the degradation of incomplete translation products and requires dissociation of the stalled ribosomes. A central event is therefore the splitting of collided ribosomes by the ribosome quality control trigger complex, RQT, by an unknown mechanism. Here we show that RQT requires accessible mRNA and the presence of a neighboring ribosome. Cryogenic electron microscopy of RQT-ribosome complexes reveals that RQT engages the 40S subunit of the lead ribosome and can switch between two conformations. We propose that the Ski2-like helicase 1 (Slh1) subunit of RQT applies a pulling force on the mRNA, causing destabilizing conformational changes of the small ribosomal subunit, ultimately resulting in subunit dissociation. Our findings provide conceptual framework for a helicase-driven ribosomal splitting mechanism.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD
History
DepositionJan 31, 2023-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16571.png

Downloads & links

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Map

FileDownload / File: emd_16571.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 560 pix.
= 585.2 Å		1.05 Å/pix.
x 560 pix.
= 585.2 Å		1.05 Å/pix.
x 560 pix.
= 585.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.617749 - 2.6446939
Average (Standard dev.)-0.0060646306 (±0.12381513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 585.19995 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16571_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16571_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16571_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ribosome with bound RQT components (Slh1, Cue3 and Rqt4)

EntireName: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
Components
  • Complex: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
    • Complex: RQT complex (Slh1, Cue3 and Rqt4)
    • Complex: ribosome

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Supramolecule #1: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)

SupramoleculeName: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#82
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #2: RQT complex (Slh1, Cue3 and Rqt4)

SupramoleculeName: RQT complex (Slh1, Cue3 and Rqt4) / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #80-#82
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: ribosome

SupramoleculeName: ribosome / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #1-#79
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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 R3/3 / Material: COPPER / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20380
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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