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- EMDB-14411: Subtomogram average of S. pombe 80S ribosomes with additional den... -

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Entry
Database: EMDB / ID: EMD-14411
TitleSubtomogram average of S. pombe 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae
Map dataSubtomogram average of 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamella
Sample
  • Complex: Subtomogram average of S. pombe 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae
Keywords80S ribosome / RIBOSOME
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsMahamid J / Goetz SK
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067European Union
CitationJournal: Nat Methods / Year: 2023
Title: Convolutional networks for supervised mining of molecular patterns within cellular context.
Authors: Irene de Teresa-Trueba / Sara K Goetz / Alexander Mattausch / Frosina Stojanovska / Christian E Zimmerli / Mauricio Toro-Nahuelpan / Dorothy W C Cheng / Fergus Tollervey / Constantin Pape / ...Authors: Irene de Teresa-Trueba / Sara K Goetz / Alexander Mattausch / Frosina Stojanovska / Christian E Zimmerli / Mauricio Toro-Nahuelpan / Dorothy W C Cheng / Fergus Tollervey / Constantin Pape / Martin Beck / Alba Diz-Muñoz / Anna Kreshuk / Julia Mahamid / Judith B Zaugg /
Abstract: Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning ...Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.
History
DepositionFeb 22, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14411.png

Downloads & links

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Map

FileDownload / File: emd_14411.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamella
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.37 Å/pix.
x 140 pix.
= 471.828 Å		3.37 Å/pix.
x 140 pix.
= 471.828 Å		3.37 Å/pix.
x 140 pix.
= 471.828 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3702 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.28851545 - 0.47855842
Average (Standard dev.)0.0033059723 (±0.04952248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 471.828 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Subtomogram average of S. pombe 80S ribosomes with additional den...

EntireName: Subtomogram average of S. pombe 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae
Components
  • Complex: Subtomogram average of S. pombe 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae

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Supramolecule #1: Subtomogram average of S. pombe 80S ribosomes with additional den...

SupramoleculeName: Subtomogram average of S. pombe 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired with a Volta potential phase plate on cryo-FIB-lamellae
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast) / Location in cell: cytoplasm

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 5755
ExtractionNumber tomograms: 10 / Number images used: 25311 / Software - Name: Warp
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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