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- EMDB-48530: Reconstruction of RQC particle with Rqc1 density -

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Basic information

Entry
Database: EMDB / ID: EMD-48530
TitleReconstruction of RQC particle with Rqc1 density
Map data
Sample
  • Complex: Structure of the eukaryotic Ribosome-associated Quality Control complex
Keywordsubiquitin / structural protein / RIBOSOMAL PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLi W / Cahoon T / Shen PS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM133772 United States
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism of nascent chain removal by the ribosome-associated quality control complex.
Authors: Wenyan Li / Talia Scheel / Peter S Shen /
Abstract: Errors during translation can cause ribosome stalling, leaving incomplete nascent chains attached to large ribosomal subunits. Cells rely on the Ribosome-associated Quality Control (RQC) complex to ...Errors during translation can cause ribosome stalling, leaving incomplete nascent chains attached to large ribosomal subunits. Cells rely on the Ribosome-associated Quality Control (RQC) complex to recognize, process, and remove these aberrant proteins to maintain proteostasis. Despite its importance, the mechanisms by which the RQC orchestrates nascent chain processing and extraction have remained unclear. Here, we present a cryo-EM structure of the RQC complex from budding yeast, revealing how its core components function in nascent chain removal. We show that the Cdc48 ATPase and its Ufd1-Npl4 adaptor are recruited by the Ltn1 E3 ubiquitin ligase to extract ubiquitylated peptides from the 60S ribosome. Additionally, we find that Rqc1 bridges the 60S subunit with ubiquitin and Ltn1, facilitating formation of K48-linked polyubiquitin chains. These findings provide a structural and mechanistic framework for understanding how the RQC complex collaborates to clear stalled translation products, advancing insight into cellular protein quality control.
History
DepositionJan 3, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48530.png

Downloads & links

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Map

FileDownload / File: emd_48530.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 640 pix.
= 677.12 Å		1.06 Å/pix.
x 640 pix.
= 677.12 Å		1.06 Å/pix.
x 640 pix.
= 677.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4935549 - 1.0854517
Average (Standard dev.)-0.00003135261 (±0.03687064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 677.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48530_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48530_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 : Structure of the eukaryotic Ribosome-associated Quality Control c...

EntireName: Structure of the eukaryotic Ribosome-associated Quality Control complex
Components
  • Complex: Structure of the eukaryotic Ribosome-associated Quality Control complex

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Supramolecule #1: Structure of the eukaryotic Ribosome-associated Quality Control c...

SupramoleculeName: Structure of the eukaryotic Ribosome-associated Quality Control complex
type: complex / ID: 1 / Parent: 0
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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14039
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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