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- EMDB-10409: In situ cryo-electron tomogram from Chlamydomonas reinhardtii of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10409
TitleIn situ cryo-electron tomogram from Chlamydomonas reinhardtii of a proteasome cluster at the endoplasmic reticulum
Map data
SampleWhole Chlamydomonas cells
Biological speciesChlamydomonas reinhardtii (plant)
Methodelectron tomography / cryo EM
AuthorsAlbert S / Schaffer M / Baumeister W / Engel BD
CitationJournal: To Be Published
Title: Direct visualization of degradation microcompartments at the ER membrane
Authors: Albert S / Wietrzynski W / Lee CW / Schaffer M / Beck F / Schuller JM / Salome PA / Plitzko JM / Baumeister W / Engel BD
History
DepositionOct 27, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing 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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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10409.map.gz / Format: CCP4 / Size: 762.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.68 Å/pix.
x 464 pix.
= 6347.52 Å
13.68 Å/pix.
x 928 pix.
= 12695.04 Å
13.68 Å/pix.
x 928 pix.
= 12695.04 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: 13.68 Å
Density
Minimum - Maximum-89 - 76
Average (Standard dev.)2.5810552 (±10.353283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00232
Dimensions928928464
Spacing928928464
CellA: 12695.04 Å / B: 12695.04 Å / C: 6347.52 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS00232
NC/NR/NS928928464
D min/max/mean-89.00076.0002.581

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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)

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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: OTHER / Details: blotted from back for 10 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Bidirectional tilt scheme, separated at 0 degrees
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 5000.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 60
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD

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