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- EMDB-3977: Cryo-electron tomogram of the Chlamydomonas reinhardtii Golgi app... -

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Basic information

Entry
Database: EMDB / ID: 3977
TitleCryo-electron tomogram of the Chlamydomonas reinhardtii Golgi apparatus
Map dataCryo-electron tomogram of Chlamydomonas reinhardtii Golgi apparatus
SampleWhole Chlamydomonas cells:
SourceChlamydomonas reinhardtii (plant)
Methodelectron tomography / cryo EM
AuthorsBykov YS / Schaffer M / Dodonova SO / Albert S / Plitzko JM / Baumeister W / Engel BD / Briggs JAG
CitationJournal: Elife / Year: 2017
Title: The structure of the COPI coat determined within the cell.
Authors: Yury S Bykov / Miroslava Schaffer / Svetlana O Dodonova / Sahradha Albert / Jürgen M Plitzko / Wolfgang Baumeister / Benjamin D Engel / John Ag Briggs
DateDeposition: Nov 7, 2017 / Header (metadata) release: Nov 15, 2017 / Map release: Nov 29, 2017 / Last update: Nov 29, 2017

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Structure visualization

Movie
  • Solid view (volume rendering)
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  • Solid view (volume rendering)
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  • Simplified surface model
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Structure viewerEM map:
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Supplemental images

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Map

Fileemd_3977.map.gz (map file in CCP4 format, 799179 KB)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
464 pix
13.68 Å/pix.
= 6347.52 Å
928 pix
13.68 Å/pix.
= 12695.04 Å
928 pix
13.68 Å/pix.
= 12695.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 13.68 Å
Density
Contour Level:0.1 (by author)
Minimum - Maximum-3282 - 2183
Average (Standard dev.)36.84576 (347.0019)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions928928464
Origin0068
Limit927927531
Spacing928928464
CellA: 12695.04 Å / B: 12695.04 Å / C: 6347.52 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z13.6813.6813.68
M x/y/z928928464
origin x/y/z0.0000.0000.000
length x/y/z12695.04012695.0406347.520
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS0068
NC/NR/NS928928464
D min/max/mean-3282.0002183.00036.846

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Supplemental data

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Sample components

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Entire Whole Chlamydomonas cells

EntireName: Whole Chlamydomonas cells
Details: Grown suspended in TAP media, with normal atmosphere aeration and constant light
Number of components: 1

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Component #1: cellular-component, Whole Chlamydomonas cells

Cellular-componentName: Whole Chlamydomonas cells
Details: Grown suspended in TAP media, with normal atmosphere aeration and constant light
Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii (plant) / Strain: mat3-4
Source (natural)Organelle: Golgi

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionBuffer solution: TAP media / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE MIXTURE / Humidity: 90 %
Details: Blotted from the back side for 10 seconds with 10 blot force before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000 - 6000 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -52 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Tilt angle increment: 2 deg. / Number of sections: 55
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD
Details: Each of the images in the tilt series was low-pass filtered according to the electron-dose acquired by the sample (Grant and Grigorieff, 2015). This is a bin4 (twice binned) tomogram. Three last tilts (56, 58, and 60 degrees) were excluded from the reconstruction.

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