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- EMDB-2661: Cryo-EM structure of the Plasmodium falciparum 80S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-2661
TitleCryo-EM structure of the Plasmodium falciparum 80S ribosome
Map dataCryo-EM map of the Plasmodium falciparum 80S ribosome
Sample
  • Sample: Plasmodium falciparum 80S ribosome
  • Complex: Plasmodium falciparum 80S ribosome
KeywordsPlasmodium falciparum 80S ribosome / Cryo-EM
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.4 Å
AuthorsWong W / Bai XC / Brown A / Fernandez IS / Hanssen E / Condron M / Tan YH / Baum J / Scheres SHW
CitationJournal: Elife / Year: 2014
Title: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
Authors: Wilson Wong / Xiao-chen Bai / Alan Brown / Israel S Fernandez / Eric Hanssen / Melanie Condron / Yan Hong Tan / Jake Baum / Sjors H W Scheres /
Abstract: Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as ...Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as potential anti-malarial therapies. Antibiotics that inhibit protein translation are promising candidates for repositioning. We have solved the cryo-EM structure of the cytoplasmic ribosome from the human malaria parasite, Plasmodium falciparum, in complex with emetine at 3.2 Å resolution. Emetine is an anti-protozoan drug used in the treatment of ameobiasis that also displays potent anti-malarial activity. Emetine interacts with the E-site of the ribosomal small subunit and shares a similar binding site with the antibiotic pactamycin, thereby delivering its therapeutic effect by blocking mRNA/tRNA translocation. As the first cryo-EM structure that visualizes an antibiotic bound to any ribosome at atomic resolution, this establishes cryo-EM as a powerful tool for screening and guiding the design of drugs that target parasite translation machinery.
History
DepositionMay 22, 2014-
Header (metadata) releaseMay 28, 2014-
Map releaseJun 18, 2014-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

cover_image_...

Downloads & links

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Map

FileDownload / File: emd_2661.map.gz / Format: CCP4 / Size: 339.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the Plasmodium falciparum 80S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 450 pix.
= 463.5 Å		1.03 Å/pix.
x 450 pix.
= 463.5 Å		1.03 Å/pix.
x 450 pix.
= 463.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-0.71674609 - 0.95444626
Average (Standard dev.)0.00000514 (±0.04286634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 463.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z463.500463.500463.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.7170.9540.000

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Supplemental data

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Supplemental map: emd 2661 half map 1.map

Fileemd_2661_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 2661 half map 2.map

Fileemd_2661_half_map_2.map
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

EntireName: Plasmodium falciparum 80S ribosome
Components
  • Sample: Plasmodium falciparum 80S ribosome
  • Complex: Plasmodium falciparum 80S ribosome

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Supramolecule #1000: Plasmodium falciparum 80S ribosome

SupramoleculeName: Plasmodium falciparum 80S ribosome / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa

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Supramolecule #1: Plasmodium falciparum 80S ribosome

SupramoleculeName: Plasmodium falciparum 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.4
Details: 20 mM Hepes pH7.4, 40 mM KCH3COO, 10 mM NH4CH3COO, 10 mM Mg(CH3COO)2 and 5 mM 2-mecaptoethanol
StainingType: NEGATIVE / Details: Cryo-EM
GridDetails: 30 s on glow-discharged holey carbon grids (Quantifoil R2/2), onto which a home-made continuous carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: Blot 2.5 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 78,000 times magnification
DateJan 28, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1307 / Average electron dose: 20 e/Å2
Details: An in-house built system was used to intercept the videos from the detector at a rate of 17 frames for the 1 s exposures.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 135922 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 78000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION
Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement.
Number images used: 72293

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