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- EMDB-50170: Stalled ribosome with Mbf1 N-terminus -

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Basic information

Entry
Database: EMDB / ID: EMD-50170
TitleStalled ribosome with Mbf1 N-terminus
Map dataStalled ribosome with Mbf1 N-terminus - local resolution filtered
Sample
  • Complex: glutaraldehyde crosslinked tri- and tetrasome fraction after sucrose density gradient centrifugation from yeast in vitro translation
Keywordsribosome / Mbf1 / collision / quality control
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsDenk T / Beckmann R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Mol Cell / Year: 2024
Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Authors: Kyusik Q Kim / Jeffrey J Li / Ankanahalli N Nanjaraj Urs / Miguel E Pacheco / Victor Lasehinde / Timo Denk / Petr Tesina / Shota Tomomatsu / Yoshitaka Matsuo / Elesa McDonald / Roland ...Authors: Kyusik Q Kim / Jeffrey J Li / Ankanahalli N Nanjaraj Urs / Miguel E Pacheco / Victor Lasehinde / Timo Denk / Petr Tesina / Shota Tomomatsu / Yoshitaka Matsuo / Elesa McDonald / Roland Beckmann / Toshifumi Inada / Rachel Green / Hani S Zaher /
Abstract: In yeast, multiprotein bridging factor 1 (Mbf1) has been proposed to function in the integrated stress response (ISR) as a transcriptional coactivator by mediating a direct interaction between ...In yeast, multiprotein bridging factor 1 (Mbf1) has been proposed to function in the integrated stress response (ISR) as a transcriptional coactivator by mediating a direct interaction between general transcription machinery and the process's key effector, Gcn4. However, mounting evidence has demonstrated that Mbf1 (and its human homolog EDF1) is recruited to collided ribosomes, a known activator of the ISR. In this study, we connect these otherwise seemingly disparate functions of Mbf1. Our biochemical and structural analyses reveal that Mbf1 functions as a core ISR factor by interacting with collided ribosomes to mediate Gcn2 activation. We further show that Mbf1 serves no role as a transcriptional coactivator of Gcn4. Instead, Mbf1 is required for optimal stress-induced eukaryotic initiation factor 2α (eIF2α) phosphorylation and downstream de-repression of GCN4 translation. Collectively, our data establish that Mbf1 functions in ISR signaling by acting as a direct sensor of stress-induced ribosome collisions.
History
DepositionApr 25, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50170.png

Downloads & links

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Map

FileDownload / File: emd_50170.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStalled ribosome with Mbf1 N-terminus - local resolution filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 450 pix.
= 470.25 Å		1.05 Å/pix.
x 450 pix.
= 470.25 Å		1.05 Å/pix.
x 450 pix.
= 470.25 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-2.9533234 - 6.4881105
Average (Standard dev.)0.028979048 (±0.17237796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 470.24997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Stalled ribosome with Mbf1 N-terminus

Fileemd_50170_additional_1.map
AnnotationStalled ribosome with Mbf1 N-terminus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Stalled ribosome with Mbf1 N-terminus - half map A

Fileemd_50170_half_map_1.map
AnnotationStalled ribosome with Mbf1 N-terminus - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Stalled ribosome with Mbf1 N-terminus - half map B

Fileemd_50170_half_map_2.map
AnnotationStalled ribosome with Mbf1 N-terminus - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : glutaraldehyde crosslinked tri- and tetrasome fraction after sucr...

EntireName: glutaraldehyde crosslinked tri- and tetrasome fraction after sucrose density gradient centrifugation from yeast in vitro translation
Components
  • Complex: glutaraldehyde crosslinked tri- and tetrasome fraction after sucrose density gradient centrifugation from yeast in vitro translation

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Supramolecule #1: glutaraldehyde crosslinked tri- and tetrasome fraction after sucr...

SupramoleculeName: glutaraldehyde crosslinked tri- and tetrasome fraction after sucrose density gradient centrifugation from yeast in vitro translation
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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / 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: 3.5 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48521
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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