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- EMDB-4375: GEM subtomogram average obtained for yeast cells treated with rap... -

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Basic information

Entry
Database: EMDB / ID: EMD-4375
TitleGEM subtomogram average obtained for yeast cells treated with rapamycin
Map dataGEM subtomogram average obtained for yeast cells treated with rapamycin
Sample
  • Complex: Genetically Encoded Multimeric nanoparticles (GEMs)
Biological speciesSaccharomyces cerevisiae W303 (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 26.3 Å
AuthorsPfeffer S / Engel BD / Schaffer M
CitationJournal: Cell / Year: 2018
Title: mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding.
Authors: Delarue M / Brittingham GP / Pfeffer S / Surovtsev IV / Pinglay S / Kennedy KJ / Schaffer M / Gutierrez JI / Sang D / Poterewicz G / Chung JK / Plitzko JM / Groves JT / Jacobs-Wagner C / Engel BD / Holt LJ
History
DepositionApr 16, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseJun 27, 2018-
UpdateJul 25, 2018-
Current statusJul 25, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

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Map

FileDownload / File: emd_4375.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGEM subtomogram average obtained for yeast cells treated with rapamycin
Voxel sizeX=Y=Z: 3.42 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.404589 - 0.5441941
Average (Standard dev.)0.001220248 (±0.07197595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 684.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z684.000684.000684.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.4050.5440.001

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Supplemental data

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Sample components

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Entire : Genetically Encoded Multimeric nanoparticles (GEMs)

EntireName: Genetically Encoded Multimeric nanoparticles (GEMs)
Components
  • Complex: Genetically Encoded Multimeric nanoparticles (GEMs)

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Supramolecule #1: Genetically Encoded Multimeric nanoparticles (GEMs)

SupramoleculeName: Genetically Encoded Multimeric nanoparticles (GEMs) / type: complex / ID: 1 / Parent: 0
Details: GEMs are homomultimeric scaffolds (Pyrococcus furious encapsulin) fused to a fluorescent protein (T- Sapphire fluorophore). GEMs self-assemble into bright, stable fluorescent particles of defined size and shape.
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV / Details: 10 seconds blot time, blot force 10.
DetailsGEMs imaged in rapamycin-treated yeast cells thinned by focused ion beam milling

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 26.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 74
ExtractionNumber tomograms: 13 / Number images used: 74 / Method: template matching + visual inspection / Software - Name: PyTom
CTF correctionSoftware - Name: PyTom
Final angle assignmentType: OTHER

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