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- EMDB-18161: Focused map of the 60S ribosomal subunit ot the Gallus gallus -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-18161
TitleFocused map of the 60S ribosomal subunit ot the Gallus gallus
Map dataFocused map of the 60S ribosomal subunit ot the Gallus gallus
Sample
  • Complex: 80S Gallus gallus ribosome from chicken embryo
Keywordstranslation / complex / eEF2 / SERBP1 / RIBOSOME
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsNurullina L / Jenner L / Myasnikov A / Yusupov M
Funding support France, 1 items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM) France
CitationJournal: To Be Published
Title: Structural insights into inactive ribosome complexes derived from cold-treated chick embryo cells
Authors: Nurullina L / Terrosu S / Jenner L / Myasnikov A / Yusupov M
History
DepositionAug 8, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18161.png

Downloads & links

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Map

FileDownload / File: emd_18161.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of the 60S ribosomal subunit ot the Gallus gallus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 580 pix.
= 465.74 Å		0.8 Å/pix.
x 580 pix.
= 465.74 Å		0.8 Å/pix.
x 580 pix.
= 465.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.803 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.369627 - 2.7345695
Average (Standard dev.)-0.0010259211 (±0.081038356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 465.74 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1

Fileemd_18161_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_18161_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S Gallus gallus ribosome from chicken embryo

EntireName: 80S Gallus gallus ribosome from chicken embryo
Components
  • Complex: 80S Gallus gallus ribosome from chicken embryo

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Supramolecule #1: 80S Gallus gallus ribosome from chicken embryo

SupramoleculeName: 80S Gallus gallus ribosome from chicken embryo / type: complex / ID: 1 / Parent: 0
Details: 28S rRNA, 5.8S rRNA, 5S rRNA, 18S rRNA,ribosomal proteins, tRNA, eEF2, SERBP1
Source (natural)Organism: Gallus gallus (chicken) / Tissue: embryo
Molecular weightTheoretical: 4.3 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 32439 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 641721
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7o7z

Final reconstructionNumber classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: cryoSPARC / Number images used: 100204
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7o7z


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient

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