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- EMDB-2660: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound... -

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Entry
Database: EMDB / ID: EMD-2660
TitleCryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Map dataCryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Sample
  • Sample: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
  • Complex: Plasmodium falciparum 80S ribosome bound to the anti- protozoan drug emetine
  • Ligand: emetine
KeywordsPlasmodium falciparum / 80S ribosome / Cryo-EM / emetine
Function / homology
Function and homology information


RMTs methylate histone arginines / Protein methylation / Translesion synthesis by REV1 / Translesion Synthesis by POLH / : / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / : / Metalloprotease DUBs ...RMTs methylate histone arginines / Protein methylation / Translesion synthesis by REV1 / Translesion Synthesis by POLH / : / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / : / Metalloprotease DUBs / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ER Quality Control Compartment (ERQC) / Iron uptake and transport / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / small-subunit processome / modification-dependent protein catabolic process / protein tag activity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome biogenesis / large ribosomal subunit / ubiquitin-dependent protein catabolic process / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / negative regulation of translation / ribosome / rRNA binding / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e ...Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal L29e protein family / Ribosomal protein S10, eukaryotic/archaeal / 40S Ribosomal protein S10 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Plectin/S10, N-terminal / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Plectin/S10 domain / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L40e superfamily / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L34e, conserved site / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L30e signature 1. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L30e, conserved site / Ribosomal protein L23, N-terminal domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S11, N-terminal / Ribosomal protein S4, KOW domain / Ribosomal_S17 N-terminal / Ribosomal protein L36e signature. / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e
Similarity search - Domain/homology
40S ribosomal protein S16 / Ribosomal protein L15 / 60S ribosomal protein L39 / 40S ribosomal protein S29, putative / Ribosomal protein L37 / 40S ribosomal protein S19 / 60S ribosomal protein L18-2, putative / 60S ribosomal protein L19 / 60S ribosomal protein L27a, putative / 60S ribosomal protein L41 ...40S ribosomal protein S16 / Ribosomal protein L15 / 60S ribosomal protein L39 / 40S ribosomal protein S29, putative / Ribosomal protein L37 / 40S ribosomal protein S19 / 60S ribosomal protein L18-2, putative / 60S ribosomal protein L19 / 60S ribosomal protein L27a, putative / 60S ribosomal protein L41 / 60S ribosomal protein L29 / 60S ribosomal protein L26, putative / 40S ribosomal protein S11, putative / 40S ribosomal protein S15A, putative / Large ribosomal subunit protein eL43 / 40S ribosomal protein S26 / Small ribosomal subunit protein eS30 / Large ribosomal subunit protein eL42 / 40S ribosomal protein S23, putative / Small ribosomal subunit protein eS12 / 60S ribosomal protein L7, putative / Small ribosomal subunit protein eS1 / 60S ribosomal protein L32 / 40S ribosomal protein S9, putative / 40S ribosomal protein S24 / 60S ribosomal protein L2 / 40S ribosomal protein S11 / 60S ribosomal protein L4 / 60S ribosomal protein L31 / 40S ribosomal protein S17, putative / 60S ribosomal protein L36 / 40S ribosomal protein S16, putative / 60S ribosomal protein L13 / Large ribosomal subunit protein eL22 / 40S ribosomal protein S5, putative / 40S ribosomal protein S10, putative / 60S ribosomal protein L11a, putative / Large ribosomal subunit protein eL34 / Ubiquitin-60S ribosomal protein L40 / 40S ribosomal protein S15 / 60S ribosomal protein L17, putative / 40S ribosomal protein S6 / 60S ribosomal protein L18a / 60S ribosomal protein L6-2, putative / 60S ribosomal protein L23, putative / 60S ribosomal protein L23 / 60S ribosomal protein L6, putative / 60S ribosomal protein L24, putative / 40S ribosomal protein S27 / 40S ribosomal protein S7 / 40S ribosomal protein S19 / 40S ribosomal protein S21 / 60S ribosomal protein L35ae, putative / 60S ribosomal protein L28 / 60S ribosomal protein L38 / 40S ribosomal protein S18, putative / 60S ribosomal protein L35, putative / 40S ribosomal protein S4 / 60S ribosomal protein L3 / Small ribosomal subunit protein uS2 / 60S ribosomal protein L30e, putative / 60S ribosomal protein L13, putative / Small ribosomal subunit protein uS10 / 40S ribosomal protein S3 / 40S ribosomal protein S28e, putative / 60S ribosomal protein L27 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L14, putative / 60S ribosomal protein L21 / 60S ribosomal protein L7a / 60S ribosomal protein L5, putative / 40S ribosomal protein S25 / 60S ribosomal protein L10, putative / 40S ribosomal protein S8
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.2 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
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  • Surface view colored by height
  • Surface level: 0.18
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  • Surface view with fitted model
  • Atomic models: PDB-3j79, PDB-3j7a
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6okk
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j79
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j7a
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6okk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2660.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-0.54547346 - 0.96249408
Average (Standard dev.)0.00017136 (±0.04406156)
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-0.5450.9620.000

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Supplemental data

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Supplemental map: run1 half1 class001 unfil.map

Filerun1_half1_class001_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Supplemental map: run1 half2 class001 unfil.map

Filerun1_half2_class001_unfil.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
Components
  • Sample: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
  • Complex: Plasmodium falciparum 80S ribosome bound to the anti- protozoan drug emetine
  • Ligand: emetine

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Supramolecule #1000: Plasmodium falciparum 80S ribosome bound to the anti-protozoan dr...

SupramoleculeName: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa

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

SupramoleculeName: Plasmodium falciparum 80S ribosome bound to the anti- protozoan drug emetine
type: complex / ID: 1
Details: the anti-protozoan drug emetine was bound to the Plasmodium falciparum 80S ribosome
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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Macromolecule #1: emetine

MacromoleculeName: emetine / type: ligand / ID: 1 / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)
Chemical component information

ChemComp-34G:
emetine / Emetine

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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 POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 104748 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 78000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 78,000 times magnification
DateJan 19, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1083 / Average electron dose: 20 e/Å2
Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement.
Experimental equipment
Model: Tecnai Polara / 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: 3.2 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: 105247
DetailsUse a newly developed statistical movie processing approach to compensate for beam-induced movement.

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