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- EMDB-9207: Plasmodium falciparum 80S ribosome bound to the anti-protozoan dr... -

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Basic information

Entry
Database: EMDB / ID: EMD-9207
TitlePlasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine using Topaz picks thresholded to t-4 (EMPIAR-10028 reprocessing)
Map dataCryosparc with Topaz t-4 picks sharpened
Sample
  • Complex: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B
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
DepositionOct 15, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseOct 24, 2018-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9207.png

Downloads & links

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Map

FileDownload / File: emd_9207.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc with Topaz t-4 picks sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 360 pix.
= 482.4 Å		1.34 Å/pix.
x 360 pix.
= 482.4 Å		1.34 Å/pix.
x 360 pix.
= 482.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.05 / Movie #1: 1.05
Minimum - Maximum-2.119978 - 5.6469507
Average (Standard dev.)0.005063913 (±0.23374401)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 482.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z482.400482.400482.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-2.1205.6470.005

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Supplemental data

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Mask #1

Fileemd_9207_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc with Topaz t-4 picks unsharpened

Fileemd_9207_additional.map
AnnotationCryosparc with Topaz t-4 picks unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryosparc with Topaz t-4 picks half map

Fileemd_9207_half_map_1.map
AnnotationCryosparc with Topaz t-4 picks half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryosparc with Topaz t-4 picks half map

Fileemd_9207_half_map_2.map
AnnotationCryosparc with Topaz t-4 picks half 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 bound to the anti-protozoan dr...

EntireName: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Components
  • Complex: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine

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Supramolecule #1: Plasmodium falciparum 80S ribosome bound to the anti-protozoan dr...

SupramoleculeName: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
type: complex / ID: 1 / Parent: 0 / Details: Topaz t-4 picks
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Plasmodium falciparum (malaria parasite P. falciparum)

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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

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
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Details: home-made continuous carbon film
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Details: Blot 2.5 seconds before plunging..

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 78000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsCryoSparc v0 homogeneous 3D refinement. No particle pre-processing.
Particle selectionNumber selected: 228460
Details: All initial particles were used in the final reconstruction; ie. no particle filtering or classification was performed.
Startup modelType of model: INSILICO MODEL / In silico model: Cryosparc v0 ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - Version: 0 / Number images used: 228460
Initial angle assignmentType: OTHER / Details: Cryosparc v0
Final angle assignmentType: OTHER / Details: Cryosparc v0

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