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- EMDB-14422: Subtomogram average of S. pombe fatty acid synthase complex predi... -

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Basic information

Entry
Database: EMDB / ID: EMD-14422
TitleSubtomogram average of S. pombe fatty acid synthase complex predicted with DeePiCt in tomograms acquired on cryo-FIB-lamellae
Map dataSubtomogram average of yeast fatty acid synthase complex predicted with DeePiCt in tomograms acquired on cryo-FIB-lamellae of S. pombe
Sample
  • Complex: yeast fatty acid synthase (FAS) inside S. pombe cells
KeywordsFAS / fatty acid synthesis / CYTOSOLIC PROTEIN
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 28.0 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 23, 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_14422.png

Downloads & links

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Map

FileDownload / File: emd_14422.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of yeast fatty acid synthase complex predicted with DeePiCt in tomograms acquired on cryo-FIB-lamellae of S. pombe
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.37 Å/pix.
x 160 pix.
= 539.232 Å		3.37 Å/pix.
x 160 pix.
= 539.232 Å		3.37 Å/pix.
x 160 pix.
= 539.232 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: 0.2
Minimum - Maximum-0.35946468 - 0.9231354
Average (Standard dev.)0.0036903007 (±0.08548337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 539.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : yeast fatty acid synthase (FAS) inside S. pombe cells

EntireName: yeast fatty acid synthase (FAS) inside S. pombe cells
Components
  • Complex: yeast fatty acid synthase (FAS) inside S. pombe cells

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Supramolecule #1: yeast fatty acid synthase (FAS) inside S. pombe cells

SupramoleculeName: yeast fatty acid synthase (FAS) inside S. pombe cells / 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 / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy 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: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 108
ExtractionNumber tomograms: 10 / Number images used: 108 / Software - Name: Warp
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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