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

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Basic information

Database: EMDB / ID: 8594
TitleAutomated tomogram annotation of PC12 cell
SamplePC12 cell
SourceRattus / mammal / image: Rattus norvegicus
Map dataAutomated tomogram annotation of PC12 cell
Methodelectron tomography
AuthorsChen M / Dai W / Schmid MF / Chiu W / Ludtke SJ
CitationNat. Methods, 2017

Nat. Methods, 2017 StrPapers
Convolutional neural networks for automated annotation of cellular cryo-electron tomograms.
Muyuan Chen / Wei Dai / Stella Y Sun / Darius Jonasch / Cynthia Y He / Michael F Schmid / Wah Chiu / Steven J Ludtke

DateDeposition: Feb 3, 2017 / Header (metadata) release: Mar 1, 2017 / Map release: Mar 1, 2017 / Last update: Sep 13, 2017

Structure visualization

  • Simplified surface model
  • Imaged by Jmol
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
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Misc. /
Supplemental images

Downloads & links


Fileemd_8594.map.gz (map file in CCP4 format, 234091 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
81 pix
28.6 Å/pix.
= 2316.6 Å
850 pix
28.6 Å/pix.
= 24310. Å
850 pix
28.6 Å/pix.
= 24310. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 28.6 Å
Contour Level:0.1 (by emdb)
Minimum - Maximum-14.392706 - 25.645239
Average (Standard dev.)-1.81239E-10 (1)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 24310 Å / B: 24310 Å / C: 2316.6 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-425-425-40
D min/max/mean-14.39325.645-0.000

Supplemental data

Sample components

Entire PC12 cell

EntireName: PC12 cell / Number of components: 1

Component #1: cellular-component, PC12 cell

Cellular-componentName: PC12 cell / Recombinant expression: No
SourceSpecies: Rattus / mammal / image: Rattus norvegicus

Experimental details

Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

Electron microscopy imaging

ImagingMicroscope: JEOL 2100
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

Image processing

ProcessingMethod: electron tomography / Number of sections: 30
3D reconstructionAlgorithm: BACK PROJECTION

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