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- EMDB-0875: Volta electron cryotomograms of cryosections of fission yeast Sch... -

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Basic information

Entry
Database: EMDB / ID: EMD-0875
TitleVolta electron cryotomograms of cryosections of fission yeast Schizosaccharomyces pombe cells, in G0 quiescence and arrested in G1 phase.
Map dataVolta electron cryotomogram of a cryosection of a G0 Schizosaccharomyces pombe cell
Sample
  • Cell: S. pombe cell in G0 quiescence
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodelectron tomography / cryo EM
AuthorsCai S / Tan Z / Nie X / Shi J / Gan L
Funding support Singapore, 2 items
OrganizationGrant numberCountry
Ministry of Education (Singapore)R-154-000-B58-112 Singapore
Ministry of Education (Singapore)R-154-000-B42-114 Singapore
CitationJournal: To Be Published
Title: Structural and biochemical analysis of G0 S. pombe nuclei
Authors: Cai S / Tan Z / Nie X / Shi J / Gan L
History
DepositionNov 24, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseDec 18, 2019-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_0875.png

Downloads & links

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Map

FileDownload / File: emd_0875.map.gz / Format: CCP4 / Size: 4.6 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationVolta electron cryotomogram of a cryosection of a G0 Schizosaccharomyces pombe cell
Voxel sizeX=Y=Z: 4.6 Å
Density
Minimum - Maximum-3723 - 2829
Average (Standard dev.)168.68185 (±266.0802)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-58
Dimensions40964096146
Spacing40964096146
CellA: 18841.6 Å / B: 18841.6 Å / C: 671.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z4.64.64.6
M x/y/z40964096146
origin x/y/z0.0000.0000.000
length x/y/z18841.60018841.600671.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS00-58
NC/NR/NS40964096146
D min/max/mean-3723.0002829.000168.682

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Supplemental data

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Additional map: Volta electron cryotomogram of a cryosection of a...

Fileemd_0875_additional.map
AnnotationVolta electron cryotomogram of a cryosection of a G1-arrested Schizosaccharomyces pombe cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Volta electron cryotomogram of a cryosection of a...

Fileemd_0875_additional_1.map
AnnotationVolta electron cryotomogram of a cryosection of a G1-arrested Schizosaccharomyces pombe cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S. pombe cell in G0 quiescence

EntireName: S. pombe cell in G0 quiescence
Components
  • Cell: S. pombe cell in G0 quiescence

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Supramolecule #1: S. pombe cell in G0 quiescence

SupramoleculeName: S. pombe cell in G0 quiescence / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast) / Strain: MBY99 (972 h-)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7 / Details: EMM-N (EMM without nitrogen)
GridMaterial: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details: The Vitrobot's cup was used to condense the ethane cryogen. Crimped copper tubes containing cell paste were held ~ 3 cm above the surface of the liquid ethane, then dropped..
High pressure freezingInstrument: OTHER
Details: The cells were self-pressurized frozen in crimped copper tubes.. The value given for _emd_high_pressure_freezing.instrument is Vitrobot cup. This is not in a list of allowed values ...Details: The cells were self-pressurized frozen in crimped copper tubes.. The value given for _emd_high_pressure_freezing.instrument is Vitrobot cup. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.
Cryo protectant30% dextran
SectioningUltramicrotomy - Instrument: Leica UC7/FC7 / Ultramicrotomy - Temperature: 123 K / Ultramicrotomy - Final thickness: 70 nm
Fiducial markerManufacturer: BBI / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 1.0 µm / Nominal magnification: 18000
Specialist opticsPhase plate: VOLTA PHASE PLATE
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 61 / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9) / Number images used: 61

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