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- EMDB-16921: 40S head focused map of Candida albicans 80S ribosome in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16921
Title40S head focused map of Candida albicans 80S ribosome in complex with mefloquine
Map data40S head focused map
Sample
  • Complex: Candida albicans 80S ribosome in complex with mefloquine
KeywordsCandida albicans / ribosome / mefloquine
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKolosova O / Zgadzay Y / Stetsenko A / Guskov A / Yusupov M
Funding support France, Russian Federation, 4 items
OrganizationGrant numberCountry
Foundation for Medical Research (France)DEQ20181039600 France
Foundation for Medical Research (France)DBF20160635745 France
Foundation for Medical Research (France)FDT202204014886 France
Russian Science Foundation20-65-47031 Russian Federation
CitationJournal: To Be Published
Title: Drug-induced rotational movement of the ribosome is a key factor for read-through enhancement
Authors: Kolosova O / Zgadzay Y / Yusupov M
History
DepositionMar 27, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16921.png

Downloads & links

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Map

FileDownload / File: emd_16921.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation40S head focused map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 420 pix.
= 428.4 Å		1.02 Å/pix.
x 420 pix.
= 428.4 Å		1.02 Å/pix.
x 420 pix.
= 428.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.179
Minimum - Maximum-1.0189004 - 1.7950826
Average (Standard dev.)-0.003485016 (±0.055063814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 428.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map 1

Fileemd_16921_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_16921_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 : Candida albicans 80S ribosome in complex with mefloquine

EntireName: Candida albicans 80S ribosome in complex with mefloquine
Components
  • Complex: Candida albicans 80S ribosome in complex with mefloquine

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Supramolecule #1: Candida albicans 80S ribosome in complex with mefloquine

SupramoleculeName: Candida albicans 80S ribosome in complex with mefloquine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#79
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 3.3 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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 16.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Talos Arctica / 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49801
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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