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- EMDB-10767: Cryo-electron tomogram and segmentation of the cortical ER in yea... -

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Basic information

Entry
Database: EMDB / ID: EMD-10767
TitleCryo-electron tomogram and segmentation of the cortical ER in yeast, used for testing surface extraction algorithms.
Map dataRaw tomogram.
Sample
  • Organelle or cellular component: Saccharomyces cerevisiae strain ANDY129 deltaScs2 deltaScs22 deltaIst2.
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsCollado JF / Salfer M
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)FP7 GA ERC-2012-387 SyG_318987-ToPAG Germany
German Research Foundation (DFG)GSC-1006 Germany
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
CitationJournal: PLoS Comput Biol / Year: 2020
Title: Reliable estimation of membrane curvature for cryo-electron tomography.
Authors: Maria Salfer / Javier F Collado / Wolfgang Baumeister / Rubén Fernández-Busnadiego / Antonio Martínez-Sánchez /
Abstract: Curvature is a fundamental morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to- ...Curvature is a fundamental morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to-native state and molecular resolution. However, current curvature estimation methods cannot be applied directly to membrane segmentations in cryo-ET, as these methods cannot cope with some of the artifacts introduced during image acquisition and membrane segmentation, such as quantization noise and open borders. Here, we developed and implemented a Python package for membrane curvature estimation from tomogram segmentations, which we named PyCurv. From a membrane segmentation, a signed surface (triangle mesh) is first extracted. The triangle mesh is then represented by a graph, which facilitates finding neighboring triangles and the calculation of geodesic distances necessary for local curvature estimation. PyCurv estimates curvature based on tensor voting. Beside curvatures, this algorithm also provides robust estimations of surface normals and principal directions. We tested PyCurv and three well-established methods on benchmark surfaces and biological data. This revealed the superior performance of PyCurv not only for cryo-ET, but also for data generated by other techniques such as light microscopy and magnetic resonance imaging. Altogether, PyCurv is a versatile open-source software to reliably estimate curvature of membranes and other surfaces in a wide variety of applications.
History
DepositionMar 15, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / 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_10767.png

Downloads & links

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Map

FileDownload / File: emd_10767.map.gz / Format: CCP4 / Size: 643.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw tomogram.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.68 Å/pix.
x 196 pix.
= 2681.28 Å		13.68 Å/pix.
x 928 pix.
= 12695.04 Å		13.68 Å/pix.
x 928 pix.
= 12695.04 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: 13.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-204.81978 - 186.58344
Average (Standard dev.)4.100616 (±18.328278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin9800
Dimensions928928196
Spacing928928196
CellA: 12695.04 Å / B: 12695.04 Å / C: 2681.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.6813.6813.68
M x/y/z928928196
origin x/y/z0.0000.0000.000
length x/y/z12695.04012695.0402681.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS0980
NC/NR/NS928928196
D min/max/mean-204.820186.5834.101

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Supplemental data

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Mask #1

Fileemd_10767_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Filtered subset of the tomogram using TOMOEED, an...

Fileemd_10767_additional.map
AnnotationFiltered subset of the tomogram using TOMOEED, an anisotropic nonlenear diffusion filter (Fernandez, Lucic 2011).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Filtered subset of the tomogram using TOMOEED, an...

Fileemd_10767_additional_1.map
AnnotationFiltered subset of the tomogram using TOMOEED, an anisotropic nonlenear diffusion filter (Fernandez, Lucic 2011).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae strain ANDY129 deltaScs2 deltaScs22 delt...

EntireName: Saccharomyces cerevisiae strain ANDY129 deltaScs2 deltaScs22 deltaIst2.
Components
  • Organelle or cellular component: Saccharomyces cerevisiae strain ANDY129 deltaScs2 deltaScs22 deltaIst2.

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Supramolecule #1: Saccharomyces cerevisiae strain ANDY129 deltaScs2 deltaScs22 delt...

SupramoleculeName: Saccharomyces cerevisiae strain ANDY129 deltaScs2 deltaScs22 deltaIst2.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Organelle: ER, plasma membrane
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: ANDY129

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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: 6
VitrificationCryogen name: ETHANE
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: 4000 sec. / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Quanta 3D Cryo-FIB / SEM. 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 TITAN KRIOS
TemperatureMin: 80.0 K / Max: 90.0 K
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 exposure time: 1.6 sec. / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 42000
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 reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 43

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