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- EMDB-18150: Cryo-EM map of the Candida albicans 80S ribosome in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18150
TitleCryo-EM map of the Candida albicans 80S ribosome in complex with cephaeline
Map dataEM map (unfocused)
Sample
  • Complex: The Candida albicans ribosome in complew with cephaeline
KeywordsRibosome / Candida albicans / cephaeline
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsKolosova O / Zgadzay Y / Stetsenko A / Atamas A / Jenner L / Guskov A / Yusupov M
Funding support France, 1 items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM)FDT202204014886 France
CitationJournal: Biopolym Cell / Year: 2023
Title: Structural characterization of cephaeline binding to the eukaryotic ribosome using Cryo-Electron Microscopy
Authors: Kolosova O / Zgadzay Y / Stetsenko A / Atamas A / Wu C / Jenner L / Sachs SM / Guskov A / Yusupov M
History
DepositionAug 7, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18150.png

Downloads & links

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Map

FileDownload / File: emd_18150.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map (unfocused)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 510 pix.
= 426.36 Å		0.84 Å/pix.
x 510 pix.
= 426.36 Å		0.84 Å/pix.
x 510 pix.
= 426.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.219
Minimum - Maximum-0.75842094 - 1.8154389
Average (Standard dev.)0.0060655237 (±0.05704835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 426.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_18150_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_18150_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The Candida albicans ribosome in complew with cephaeline

EntireName: The Candida albicans ribosome in complew with cephaeline
Components
  • Complex: The Candida albicans ribosome in complew with cephaeline

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Supramolecule #1: The Candida albicans ribosome in complew with cephaeline

SupramoleculeName: The Candida albicans ribosome in complew with cephaeline
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Candida albicans (yeast)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7pzy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 254047
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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