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- EMDB-8594: Automated tomogram annotation of PC12 cell -

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Basic information

Entry
Database: EMDB / ID: EMD-8594
TitleAutomated tomogram annotation of PC12 cell
Map dataAutomated tomogram annotation of PC12 cell
Sample
  • Cell: PC12 cell
Biological speciesRattus (rats)
Methodelectron tomography / cryo EM
AuthorsChen M / Dai W / Schmid MF / Chiu W / Ludtke SJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139, P01NS092525, P41GM103832 United States
CitationJournal: Nat Methods / Year: 2017
Title: Convolutional neural networks for automated annotation of cellular cryo-electron tomograms.
Authors: Muyuan Chen / Wei Dai / Stella Y Sun / Darius Jonasch / Cynthia Y He / Michael F Schmid / Wah Chiu / Steven J Ludtke /
Abstract: Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components ...Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components within the crowded cellular environment. We introduce a method that uses neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yield in situ structures of molecular components of interest. The method is available in the EMAN2.2 software package.
History
DepositionFeb 3, 2017-
Header (metadata) releaseMar 1, 2017-
Map releaseMar 1, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing 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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  • Simplified surface model
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8594.png

Downloads & links

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Map

FileDownload / File: emd_8594.map.gz / Format: CCP4 / Size: 223.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAutomated tomogram annotation of PC12 cell
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
28.6 Å/pix.
x 81 pix.
= 2316.6 Å		28.6 Å/pix.
x 850 pix.
= 24310. Å		28.6 Å/pix.
x 850 pix.
= 24310. 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: 28.6 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-14.392706 - 25.645239
Average (Standard dev.)-0.1812393800 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-425-425-40
Dimensions85085081
Spacing85085081
CellA: 24310.0 Å / B: 24310.0 Å / C: 2316.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z28.628.628.6
M x/y/z85085081
origin x/y/z0.0000.0000.000
length x/y/z24310.00024310.0002316.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-425-425-40
NC/NR/NS85085081
D min/max/mean-14.39325.645-0.000

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Supplemental data

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Additional map: Automatic annotation of double layer membrane in PC12 cell

Fileemd_8594_additional_1.map
AnnotationAutomatic annotation of double layer membrane in PC12 cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Automatic annotation of microtubules in PC12 cell

Fileemd_8594_additional_2.map
AnnotationAutomatic annotation of microtubules in PC12 cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Automatic annotation of ribosomes in PC12 cell

Fileemd_8594_additional_3.map
AnnotationAutomatic annotation of ribosomes in PC12 cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Automatic annotation of single layer membrane in PC12 cell

Fileemd_8594_additional_4.map
AnnotationAutomatic annotation of single layer membrane in PC12 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 : PC12 cell

EntireName: PC12 cell
Components
  • Cell: PC12 cell

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Supramolecule #1: PC12 cell

SupramoleculeName: PC12 cell / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Rattus (rats)

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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
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 14 nm

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Electron microscopy

MicroscopeJEOL 2100
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 30

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