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- EMDB-9208: Plasmodium falciparum 80S ribosome bound to the anti-protozoan dr... -

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Basic information

Entry
Database: EMDB / ID: EMD-9208
TitlePlasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine using (Topaz t-2) - (published) picks (EMPIAR-10028 reprocessing)
Map data
SamplePlasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsBepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B
Citation
Journal: Res Comput Mol Biol / Year: 2018
Title: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.
Authors: Tristan Bepler / Andrew Morin / Alex J Noble / Julia Brasch / Lawrence Shapiro / Bonnie Berger /
#1: Journal: 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: 0.592
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.592
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9208.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 400 pix.
= 536. Å
1.34 Å/pix.
x 400 pix.
= 536. Å
1.34 Å/pix.
x 400 pix.
= 536. 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
Contour LevelBy AUTHOR: 0.592 / Movie #1: 0.592
Minimum - Maximum-1.3735771 - 4.0049515
Average (Standard dev.)0.00008160598 (±0.16336381)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 536.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.3744.0050.000

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Supplemental data

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Segmentation: #1

Fileemd_9208_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Cryosparc v0 with (Topaz t-4) - (published) picks unsharpened

Fileemd_9208_additional.map
AnnotationCryosparc v0 with (Topaz t-4) - (published) picks unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Cryosparc v0 with (Topaz t-4) - (published) picks half map

Fileemd_9208_half_map_1.map
AnnotationCryosparc v0 with (Topaz t-4) - (published) picks half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Cryosparc v0 with (Topaz t-4) - (published) picks half map

Fileemd_9208_half_map_2.map
AnnotationCryosparc v0 with (Topaz t-4) - (published) picks half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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
Details: (Topaz t-2) - (published) picks / Number of components: 1

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Component #1: protein, Plasmodium falciparum 80S ribosome bound to the anti-pro...

ProteinName: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Details: (Topaz t-2) - (published) picks / Recombinant expression: No
SourceSpecies: Plasmodium falciparum (malaria parasite P. falciparum)
Source (engineered)Expression System: Plasmodium falciparum (malaria parasite P. falciparum)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.6 mg/mL
Buffer solution: 20 mM Hepes pH7.4, 40 mM KCH3COO, 10 mM NH4CH3COO, 10 mM Mg(CH3COO)2 and 5 mM 2-mecaptoethanol
pH: 7.4
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: Blot 2.5 seconds before plunging..

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000.0 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 3800.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 122556
Details: CryoSparc v0 homogeneous 3D refinement. No particle pre-processing.
3D reconstructionSoftware: cryoSPARC / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Cryosparc v0

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