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- EMDB-3967: In situ cryo-electron tomogram from Chlamydomonas reinhardtii of ... -

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Entry
Database: EMDB / ID: 3967
TitleIn situ cryo-electron tomogram from Chlamydomonas reinhardtii of the cellular environment around the nuclear envelope
SampleWhole Chlamydomonas cells
SourceChlamydomonas reinhardtii / plant
Map dataCryo-electron tomogram of Chlamydomonas reinhardtii nuclear membrane
Methodelectron tomography
AuthorsAlbert S / Schaffer M / Beck F / Mosalaganti S / Asano S / Thomas HF / Plitzko J / Beck M / Baumeister W / Engel BD
CitationProc.Natl.Acad.Sci.Usa, 2017

Proc.Natl.Acad.Sci.Usa, 2017
Proteasomes tether to two distinct sites at the nuclear pore complex
Albert S / Schaffer M / Beck F / Mosalaganti S / Asano S / Thomas HF / Plitzko J / Beck M / Baumeister W / Engel BD

DateDeposition: Nov 7, 2017 / Header (metadata) release: Nov 15, 2017 / Map release: Nov 22, 2017 / Last update: Dec 13, 2017

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Map

Fileemd_3967.map.gz (map file in CCP4 format, 799179 KB)
Projections & slices

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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

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 13.68 Å
Density
Contour Level:15 (by author)
Minimum - Maximum-112 - 109
Average (Standard dev.)2.7339582 (10.788662)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions928928464
Origin00232
Limit927927695
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/NS00232
NC/NR/NS928928464
D min/max/mean-112.000109.0002.734

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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

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Experimental details

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Sample preparation

Specimen statecell
Sample solutionBuffer solution: TAP media / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 293 K / Humidity: 90 %
Details: Blotted 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: -60 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionDetails: Images were collected in movie mode at 12 frames per second

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Image processing

ProcessingMethod: electron tomography / Tilt angle increment: 2 deg. / Number of sections: 61
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD / Details: This is a bin4 (twice binned) tomogram.

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

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