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

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Basic information

Entry
Database: EMDB / ID: 8589
TitleSubtomogram average of microtubules from Trypanosoma brucei
SampleMicrotubule
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, 14, 983-985

Nat. Methods, 2017, 14, 983-985 Yorodumi Papers
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: Oct 11, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

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

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
230 pix
1.05 Å/pix.
= 240.35 Å
230 pix
1.05 Å/pix.
= 240.35 Å
230 pix
1.05 Å/pix.
= 240.35 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider package.

Voxel size
XYZ
EMDB info.5.35.35.3
CCP4 map header1.0451.0451.045
EM Navigator Movie #11.0451.0451.045
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.12275627 - 0.17894378
Average (Standard dev.)0.00026404572 (0.019319996)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin2.29552e+065.97019e+06968033
Limit2.29571e+065.97038e+06968224
Spacing192192192
CellA=B=C: 1017.60004 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z240.350240.350240.350
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.4550.8160.004

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Supplemental data

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Sample components

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Entire Microtubule

EntireName: Microtubule / Number of components: 1

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Component #1: protein, Microtubule

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

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Experimental details

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Sample preparation

Specimen statecell
Sample solutionpH: 7.2
VitrificationCryogen name: ETHANE

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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)

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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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  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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