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- EMDB-8589: Subtomogram average of microtubules from Trypanosoma brucei -

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Basic information

Database: EMDB / ID: 8589
TitleSubtomogram average of microtubules from Trypanosoma brucei
SourceTrypanosoma brucei / eukaryote /
Map dataSubtomogram average of microtubules from Trypanosoma brucei
Methodsubtomogram averaging, at 55 Å resolution
AuthorsChen M / Sun SY / Ludtke SJ / He CY / Schmid MF / Chiu W
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

  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8589.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
280 pix
2.49 Å/pix.
= 698.326 Å
280 pix
2.49 Å/pix.
= 698.326 Å
280 pix
2.49 Å/pix.
= 698.326 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel size
EMDB info.
CCP4 map header2.494022.494022.49402
EM Navigator Movie #12.494022.494022.49402
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.12275627 - 0.17894378
Average (Standard dev.)0.00026404572 (0.019319996)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1017.60004 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.49402142857142.49402142857142.4940214285714
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z698.326698.326698.326
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-140-140-140
D min/max/mean0.0000.2130.007

Supplemental data

Sample components

Entire Microtubule

EntireName: Microtubule / Number of components: 1

Component #1: protein, Microtubule

ProteinName: Microtubule / Recombinant expression: No
SourceSpecies: Trypanosoma brucei / eukaryote /

Experimental details

Sample preparation

Specimen statecell
Sample solutionpH: 7.2
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: DIRECT ELECTRON DE-12 (4k x 3k)

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: BACK PROJECTION / Software: EMAN / Resolution: 55 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Single particle tomography tool in EMAN2

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