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- EMDB-4758: Subtomogram average of cytosolic ribosomes after cryo-FIB lift-ou... -

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Basic information

Entry
Database: EMDB / ID: EMD-4758
TitleSubtomogram average of cytosolic ribosomes after cryo-FIB lift-out (p2 state)
Map data
SampleCytosolic ribosome in the native cellular environment after cryo-FIB lift-out from C. elegans (p2 state)
Biological speciesCaenorhabditis elegans (roundworm)
Methodsubtomogram averaging / cryo EM / Resolution: 15.6 Å
AuthorsPfeffer S / Mahamid J / Albert S / Plitzko JM
CitationJournal: To Be Published
Title: A cryo-focused ion beam lift-out technique for cryo-ET reveals Ribosome structural diversity in C. elegans
Authors: Schaffer M / Pfeffer S / Mahamid J / Kleindiek S / Laugks T / Albert S / Engel B / Rummel A / Smith AJ / Baumeister W / Plitzko JM
DateDeposition: Apr 1, 2019 / Header (metadata) release: Jul 10, 2019 / Map release: Jul 10, 2019 / Update: Jul 10, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4758.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.42 Å/pix.
x 128 pix.
= 437.76 Å
3.42 Å/pix.
x 128 pix.
= 437.76 Å
3.42 Å/pix.
x 128 pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-0.562592 - 1.5158919
Average (Standard dev.)0.0053565535 (±0.17896912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z437.760437.760437.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.5631.5160.005

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Supplemental data

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Sample components

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Entire Cytosolic ribosome in the native cellular environment after cryo-...

EntireName: Cytosolic ribosome in the native cellular environment after cryo-FIB lift-out from C. elegans (p2 state)
Number of components: 1

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Component #1: protein, Cytosolic ribosome in the native cellular environment af...

ProteinName: Cytosolic ribosome in the native cellular environment after cryo-FIB lift-out from C. elegans (p2 state)
Recombinant expression: No
SourceSpecies: Caenorhabditis elegans (roundworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Tissue / Method: cryo EM
Sample solutionpH: 7.3
VitrificationCryogen name: NITROGEN
Details: The sample was high pressure frozen in a BAL-TEC HPM 100 high-pressure freezer..

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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
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 5503
3D reconstructionSoftware: RELION / Resolution: 15.6 Å / Resolution method: FSC 0.143 CUT-OFF

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