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- EMDB-51682: 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC mach... -

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Basic information

Entry
Database: EMDB / ID: EMD-51682
Title60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (60S body)
Map data
Sample
  • Complex: 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1
Keywords60S / UFMylation / ER / RQC / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPenchev I / Gumbin S / Becker T / Kopito R / Beckmann R
Funding supportEuropean Union, Germany, United States, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
German Research Foundation (DFG) Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2025
Title: UFMylation orchestrates spatiotemporal coordination of RQC at the ER.
Authors: Ivan Penchev / Samantha Gumbin / Francesco Scavone / Otto Berninghausen / Thomas Becker / Ron Kopito / Roland Beckmann /
Abstract: Degradation of arrest peptides from endoplasmic reticulum (ER) translocon-bound 60 ribosomal subunits via the ribosome-associated quality control (ER-RQC) pathway requires covalent modification of ...Degradation of arrest peptides from endoplasmic reticulum (ER) translocon-bound 60 ribosomal subunits via the ribosome-associated quality control (ER-RQC) pathway requires covalent modification of RPL26/uL24 on 60 ribosomal subunits with UFM1. However, the underlying mechanism that coordinates the UFMylation and RQC pathways remains elusive. Structural analysis of ER-RQC intermediates revealed concomitant binding and direct interaction of the UFMylation and RQC machineries on the 60. In the presence of an arrested peptidyl-transfer RNA, the RQC factor NEMF and the UFM1 E3 ligase (E3) form a direct interaction via the UFL1 subunit of E3, and UFL1 adopts a conformation distinct from that previously observed for posttermination 60. While this concomitant binding occurs on translocon-bound 60, LTN1 recruitment and arrest peptide degradation require UFMylation-dependent 60 dissociation from the translocon. These data reveal a mechanism by which the UFMylation cycle orchestrates ER-RQC.
History
DepositionOct 1, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51682.png

Downloads & links

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Map

FileDownload / File: emd_51682.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0118
Minimum - Maximum-0.05080535 - 0.057462744
Average (Standard dev.)0.00038655067 (±0.0036652563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 436.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51682_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_51682_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC mach...

EntireName: 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1
Components
  • Complex: 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1

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Supramolecule #1: 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC mach...

SupramoleculeName: 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#56
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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8461
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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