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- EMDB-14102: Microtubules in presence of 15 uM tubulin and GMPCPP seeds -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-14102
TitleMicrotubules in presence of 15 uM tubulin and GMPCPP seeds
Map data
Sample
  • Complex: Microtubules and tubulin
Biological speciesSus scrofa domesticus (domestic pig)
Methodelectron tomography / cryo EM
AuthorsVolkov VA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)609822European Union
CitationJournal: BioRxiv / Year: 2021
Title: Microtubules in presence of 15 uM tubulin and GMPCPP-stabilized seeds
Authors: Volkov VA
History
DepositionJan 2, 2022-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJan 12, 2022-
Current statusJan 12, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_14102.png

Downloads & links

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Map

FileDownload / File: emd_14102.map.gz / Format: CCP4 / Size: 3.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.34 Å/pix.
x 231 pix.
= 1695.54 Å		7.34 Å/pix.
x 1920 pix.
= 14092.801 Å		7.34 Å/pix.
x 1856 pix.
= 13623.04 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: 7.34 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-568.4244 - 358.93985
Average (Standard dev.)1.4432179 (±32.08814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-3231-116
Dimensions19201856231
Spacing18561920231
CellA: 13623.04 Å / B: 14092.801 Å / C: 1695.54 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.347.34000052083337.34
M x/y/z18561920231
origin x/y/z0.0000.0000.000
length x/y/z13623.04014092.8011695.540
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS31-32-116
NC/NR/NS18561920231
D min/max/mean-568.424358.9401.443

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Supplemental data

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Sample components

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Entire : Microtubules and tubulin

EntireName: Microtubules and tubulin
Components
  • Complex: Microtubules and tubulin

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Supramolecule #1: Microtubules and tubulin

SupramoleculeName: Microtubules and tubulin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa domesticus (domestic pig)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 6.9
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Sigma / Diameter: 5 nm

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionNumber images used: 61

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