RCSB PDB - 3J79: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, large subunit

 3J79

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, large subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.

Wong, W.Bai, X.C.Brown, A.Fernandez, I.S.Hanssen, E.Condron, M.Tan, Y.H.Baum, J.Scheres, S.H.

(2014) Elife 3: e03080-e03080

  • DOI: https://doi.org/10.7554/eLife.03080
  • Primary Citation of Related Structures:  
    3J79, 3J7A, 6OKK

  • PubMed 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 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.


  • Organizational Affiliation

    Division of Infection and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL2260Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8I3T9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL3386Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IJC6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL4411Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8I431 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL5173Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL6190Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IE85 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL6221Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL8283Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL13202Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL13215Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL14139Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL14165Plasmodium falciparum 3D7Mutation(s): 0 
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Find proteins for Q8ILE8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL15148Plasmodium falciparum 3D7Mutation(s): 0 
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Find proteins for C6KT23 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL15205Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL16219Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8ILV2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL18294Plasmodium falciparum 3D7Mutation(s): 0 
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Find proteins for Q8ILL3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL18187Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for C0H5G3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL19182Plasmodium falciparum 3D7Mutation(s): 0 
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Find proteins for C6KSY6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL20184Plasmodium falciparum 3D7Mutation(s): 0 
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Find proteins for Q8IDS6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL21161Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8ILK3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL22203Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IDI5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL22139Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IB51 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL23190Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IE82 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL24126Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for O77364 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL24AA [auth 0]162Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IEM3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL27BA [auth 1]146Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IKM5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL28CA [auth 2]127Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IHU0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL29DA [auth 3]124Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL29EA [auth 4]67Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL30FA [auth 5]257Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL30GA [auth 6]108Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL31HA [auth 7]120Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL32IA [auth 8]131Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL33JA [auth 9]140Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL34KA [auth a]150Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL36LA [auth b]112Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL37MA [auth c]92Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL38NA [auth d]87Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL39OA [auth e]51Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL40PA [auth f]128Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL41QA [auth g]39Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL43RA [auth h]96Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL44SA [auth i]104Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AH [auth a],
BH [auth c],
CH [auth f],
DH [auth h],
EH [auth i]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2014-12-17
    Changes: Other
  • Version 1.3: 2015-06-03
    Changes: Database references
  • Version 1.4: 2018-07-18
    Changes: Data collection
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references, Derived calculations