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- EMDB-16903: 60S ribosomal subunit bound to the E3-UFM1 complex (native, UFM1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16903
Title60S ribosomal subunit bound to the E3-UFM1 complex (native, UFM1 pulldown)
Map data
Sample
  • Complex: 60S ribosomal subunit bound to the E3-UFM1 complex
KeywordsRIBOSOME / UFMylation / ER / Recycling
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPenchev I / DaRosa PA / Becker T / Beckmann R / Kopito R
Funding supportEuropean Union, Germany, United Kingdom, United States, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
German Research Foundation (DFG) Germany
The Lister Institute of Preventive Medicine United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Nature / Year: 2024
Title: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER.
Authors: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / ...Authors: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / Roland Beckmann / Ron R Kopito /
Abstract: Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that ...Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER). UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane.
History
DepositionMar 23, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16903.png

Downloads & links

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Map

FileDownload / File: emd_16903.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 376.2 Å		1.05 Å/pix.
x 360 pix.
= 376.2 Å		1.05 Å/pix.
x 360 pix.
= 376.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.015749188 - 0.081740074
Average (Standard dev.)0.0015412072 (±0.005931673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 376.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16903_half_map_1.map
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Half map: #2

Fileemd_16903_half_map_2.map
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Sample components

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Entire : 60S ribosomal subunit bound to the E3-UFM1 complex

EntireName: 60S ribosomal subunit bound to the E3-UFM1 complex
Components
  • Complex: 60S ribosomal subunit bound to the E3-UFM1 complex

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Supramolecule #1: 60S ribosomal subunit bound to the E3-UFM1 complex

SupramoleculeName: 60S ribosomal subunit bound to the E3-UFM1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#53
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 46.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14144

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