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- EMDB-8593: Subtomogram average of microtubules from Human platelet -

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Basic information

Database: EMDB / ID: 8593
TitleSubtomogram average of microtubules from Human platelet
SampleMicrotubule from Human platelet cells
SourceHomo sapiens / human
Map dataSubtomogram average of microtubules from Human platelet
Methodsubtomogram averaging, at 80 Å resolution
AuthorsChen M / Wang R / Schmid MF / Chiu W / Ludtke SJ
CitationNat. Methods, 2017

primary. 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

1. Proc. Natl. Acad. Sci. U.S.A., 2015, 112, 14266-14271 StrPapers
Electron cryotomography reveals ultrastructure alterations in platelets from patients with ovarian cancer.
Rui Wang / Rebecca L Stone / Jason T Kaelber / Ryan H Rochat / Alpa M Nick / K Vinod Vijayan / Vahid Afshar-Kharghan / Michael F Schmid / Jing-Fei Dong / Anil K Sood / Wah Chiu

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

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8593.map.gz (map file in CCP4 format, 3539 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
48 pix
14.3 Å/pix.
= 686.4 Å
48 pix
14.3 Å/pix.
= 686.4 Å
48 pix
14.3 Å/pix.
= 686.4 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel size
EMDB info.121212
CCP4 map header14.314.314.3
EM Navigator Movie #114.314.314.3
Contour Level:0.25 (by author), 0.25 (movie #1):
Minimum - Maximum-1.1433123 - 0.80589217
Average (Standard dev.)-0.0020447979 (0.12463027)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1152 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z14.314.314.3
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z686.400686.400686.400
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-24-24-24
D min/max/mean-1.6781.791-0.003

Supplemental data

Sample components

Entire Microtubule from Human platelet cells

EntireName: Microtubule from Human platelet cells / Number of components: 1

Component #1: cellular-component, Microtubule from Human platelet cells

Cellular-componentName: Microtubule from Human platelet cells / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (natural)Organ or tissue: platelet

Experimental details

Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
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: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: BACK PROJECTION / Software: EMAN / Resolution: 80 Å / Resolution method: FSC 0.143 CUT-OFF

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