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- EMDB-41488: Subtomogram averaged classical iPRE state of the malarial 80S rib... -

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Basic information

Entry
Database: EMDB / ID: EMD-41488
TitleSubtomogram averaged classical iPRE state of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes
Map dataPlasmodium falciparum classical iPRE postprocessed
Sample
  • Complex: Plasmodium falciparum 80S ribosome consensus structure
Keywordsribosome / malaria / cryoET / in situ / Plasmodium falciparum / TRANSLATION
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 5.2 Å
AuthorsAnton L / Cheng W / Zhu X / Ho CM
Funding support United States, Switzerland, France, 3 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD029613 United States
Swiss National Science Foundation Switzerland
Human Frontier Science Program (HFSP) France
CitationJournal: To Be Published
Title: Divergent translational landscape reflects adaptation to biased codon usage in malaria parasites
Authors: Anton L / Cheng W / Haile M / Cobb DW / Zhu X / Han L / Li E / Nair A / Lee CL / Ho CM
History
DepositionAug 5, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41488.png

Downloads & links

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Map

FileDownload / File: emd_41488.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasmodium falciparum classical iPRE postprocessed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.09 Å/pix.
x 240 pix.
= 502.56 Å		2.09 Å/pix.
x 240 pix.
= 502.56 Å		2.09 Å/pix.
x 240 pix.
= 502.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.094 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.529
Minimum - Maximum-0.62696636 - 1.6766737
Average (Standard dev.)0.017760543 (±0.09477008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 502.56003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Plasmodium falciparum classical iPRE half map 1

Fileemd_41488_half_map_1.map
AnnotationPlasmodium falciparum classical iPRE half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Plasmodium falciparum classical iPRE half map 2

Fileemd_41488_half_map_2.map
AnnotationPlasmodium falciparum classical iPRE half 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 : Plasmodium falciparum 80S ribosome consensus structure

EntireName: Plasmodium falciparum 80S ribosome consensus structure
Components
  • Complex: Plasmodium falciparum 80S ribosome consensus structure

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Supramolecule #1: Plasmodium falciparum 80S ribosome consensus structure

SupramoleculeName: Plasmodium falciparum 80S ribosome consensus structure
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#79
Details: Subtomogram averaged consensus structure of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.93 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.8000000000000003 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 10787
ExtractionNumber tomograms: 848 / Number images used: 129617
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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