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- EMDB-19351: Translating 80S ribosome purified from human mesenchymal cells. R... -

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Basic information

Entry
Database: EMDB / ID: EMD-19351
TitleTranslating 80S ribosome purified from human mesenchymal cells. Rotated PRE conformation with A/P and P/E tRNAs,mRNAs and neosynthesized peptides.
Map dataSharpened map of Human translating 80S purified from mesenchymal cells.
Sample
  • Complex: translating 80S ribosome purified from human mammary epithelial cell (hMEC) overexpressing ZEB1. Rotated PRE conformation with A/P and P/E tRNAs,mRNAs and neosynthesized peptides.
KeywordsEMT / ribosome heterogeneity / ZEB1 / RPL36A / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsMorin C / Baudin-Baillieu A / Nguyen Van Long F / Isaac C / Bidou L / Arbes H / Francois P / Pommier R / Adrait A / Saku A ...Morin C / Baudin-Baillieu A / Nguyen Van Long F / Isaac C / Bidou L / Arbes H / Francois P / Pommier R / Adrait A / Saku A / Gran-Ruaz S / Machkouri C / Catez F / Morel AP / Coute Y / Chat S / Giudice E / Gillet R / Puisieux A / Moyret-Lalle C / Diaz JJ / Namy O / Marcel V
Funding support France, 10 items
OrganizationGrant numberCountry
Institut National du Cancer (inCA)ARC_INCa_LNCC_7625 France
Institut National du Cancer (inCA)PRT-K EMT-CoNCEPT France
Institut National du Cancer (inCA)K17_2018-024 France
Institut National du Cancer (inCA)PLBIO 2019-138 France
Institut National du Cancer (inCA)PLBIO 2019-178 France
Institut National du Cancer (inCA)cancer_128003 France
Institut National du Cancer (inCA)LyRICAN+ France
Laboratories of Excellence (LabEx)DEVweCAN France
La ligue contre le cancerRegion Gran Ouest 2019 France
Fondation pour la Recherche Medicale (FRM)EQU202203014663 France
CitationJournal: To Be Published
Title: Translational reprogramming during epithelial-mesenchymal transition is associated with fine-tuning of ribosome composition.
Authors: Morin C / Baudin-Baillieu A / Nguyen Van Long F / Isaac C / Bidou L / Arbes H / Francois P / Pommier R / Adrait A / Saku A / Gran-Ruaz S / Machkouri C / Catez F / Morel AP / Coute Y / Chat S ...Authors: Morin C / Baudin-Baillieu A / Nguyen Van Long F / Isaac C / Bidou L / Arbes H / Francois P / Pommier R / Adrait A / Saku A / Gran-Ruaz S / Machkouri C / Catez F / Morel AP / Coute Y / Chat S / Giudice E / Gillet R / Puisieux A / Moyret-Lalle C / Diaz JJ / Namy O / Marcel V
History
DepositionJan 5, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19351.png

Downloads & links

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Map

FileDownload / File: emd_19351.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Human translating 80S purified from mesenchymal cells.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 441.344 Å		0.86 Å/pix.
x 512 pix.
= 441.344 Å		0.86 Å/pix.
x 512 pix.
= 441.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.53426856 - 0.9320135
Average (Standard dev.)0.004167569 (±0.045213707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 441.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19351_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw map of Human translating 80S purified from mesenchymal cells.

Fileemd_19351_additional_1.map
AnnotationRaw map of Human translating 80S purified from mesenchymal cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (even) of Human translating 80S purified...

Fileemd_19351_half_map_1.map
AnnotationHalf map (even) of Human translating 80S purified from mesenchymal cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (odd) of Human translating 80S purified...

Fileemd_19351_half_map_2.map
AnnotationHalf map (odd) of Human translating 80S purified from mesenchymal cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : translating 80S ribosome purified from human mammary epithelial c...

EntireName: translating 80S ribosome purified from human mammary epithelial cell (hMEC) overexpressing ZEB1. Rotated PRE conformation with A/P and P/E tRNAs,mRNAs and neosynthesized peptides.
Components
  • Complex: translating 80S ribosome purified from human mammary epithelial cell (hMEC) overexpressing ZEB1. Rotated PRE conformation with A/P and P/E tRNAs,mRNAs and neosynthesized peptides.

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Supramolecule #1: translating 80S ribosome purified from human mammary epithelial c...

SupramoleculeName: translating 80S ribosome purified from human mammary epithelial cell (hMEC) overexpressing ZEB1. Rotated PRE conformation with A/P and P/E tRNAs,mRNAs and neosynthesized peptides.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: hMEC

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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: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris-HCL
5.0 mMMagnesium dichlorideMgCl2
25.0 mMPotassium chlorideKCl
1.0 mMDTT
GridModel: Quantifoil / Material: COPPER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 10662 / Average electron dose: 54.69 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 259877
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 49633
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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