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- EMDB-24433: Yeast Nucleus Tomogram -

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Basic information

Entry
Database: EMDB / ID: EMD-24433
TitleYeast Nucleus Tomogram
Map data
Sample
  • Cell: Yeast Nuclear Periphery and Adjacent Cytosol
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsCroxford M / Villa E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP2 GM123494 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Entropy-regularized deconvolution of cellular cryotransmission electron tomograms.
Authors: Matthew Croxford / Michael Elbaum / Muthuvel Arigovindan / Zvi Kam / David Agard / Elizabeth Villa / John Sedat /
Abstract: Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in ...Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy-regularized deconvolution (ER-DC) to cryo-ET data generated from transmission electron microscopy (TEM) and reconstructed using weighted back projection (WBP). We applied deconvolution to several in situ cryo-ET datasets and assessed the results by Fourier analysis and subtomogram analysis (STA).
History
DepositionJul 13, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: RCSB / 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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Movie viewer
Supplemental images

emd_24433.png

Downloads & links

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Map

FileDownload / File: emd_24433.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.62 Å/pix.
x 928 pix.
= 9855.36 Å		10.62 Å/pix.
x 375 pix.
= 3982.5 Å		10.62 Å/pix.
x 960 pix.
= 10195.2 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.62 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.0202878 - 0.02639134
Average (Standard dev.)0.0075751776 (±0.0025985334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions375960928
Spacing960375928
CellA: 10195.2 Å / B: 3982.5 Å / C: 9855.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.6210.6210.62
M x/y/z960375928
origin x/y/z0.0000.0000.000
length x/y/z10195.2003982.5009855.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS960375928
D min/max/mean-0.0200.0260.008

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Supplemental data

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Sample components

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Entire : Yeast Nuclear Periphery and Adjacent Cytosol

EntireName: Yeast Nuclear Periphery and Adjacent Cytosol
Components
  • Cell: Yeast Nuclear Periphery and Adjacent Cytosol

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Supramolecule #1: Yeast Nuclear Periphery and Adjacent Cytosol

SupramoleculeName: Yeast Nuclear Periphery and Adjacent Cytosol / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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: 7.4
GridModel: Quantifoil / Material: COPPER
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.03 nA / Focused ion beam - Duration: 1000 sec. / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 4000 nm / Focused ion beam - Final thickness: 350 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Scios FIB. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 56

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