6OKK

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • DOI: 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 ...

    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

    Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aB262Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: MAL3P7.35PFC1020c
Find proteins for O97313 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAC263Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF10_0264
Find proteins for Q8IJD4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D221Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1465900
Find proteins for Q8IKH8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9E189Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0520000
Find proteins for Q8I3R0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4F261Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1105400
Find proteins for Q8IIU8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5G272Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1447000
Find proteins for Q8IL02 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6H306Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1342000
Find proteins for Q8IDR9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5I195Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0721600
Find proteins for Q8IBN5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7J194Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1302800
Find proteins for Q8IET7 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8L218Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1408600
Find proteins for Q8IM10 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16M144Plasmodium falciparum 3D7Mutation(s): 0 
Find proteins for A0A0L7M7C8 (Plasmodium falciparum (isolate Dd2))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20eN118Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1003500
Find proteins for Q8IK02 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10O137Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719700
Find proteins for Q8IBQ5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11P151Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23Q145Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0306900
Find proteins for O97248 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12R141Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPS12MAL3P2.28PFC0295C
Find proteins for O97249 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18S156Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1126200
Find proteins for Q8IIA2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29T54Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0705700
Find proteins for C0H4K8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15U151Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1358800
Find proteins for Q8IDB0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11V161Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0317600
Find proteins for O77381 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17W137Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1242700
Find proteins for Q8I502 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19X145Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1317800
Find proteins for C0H5C2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19Y170Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0422400
Find proteins for Q8IFP2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21Z82Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144000
Find proteins for Q8IHS5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24a133Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0519400
Find proteins for Q8I3R6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25b105Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1421200
Find proteins for Q8ILN8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26c107Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0217800
Find proteins for O96258 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27d82Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1308300
Find proteins for Q8IEN2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28ee67Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1461300
Find proteins for Q8IKL9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30f58Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPS30PFB0885w
Find proteins for O96269 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15AK130Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0316800
Find proteins for O77395 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA2092Plasmodium falciparum 3D7
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Entity ID: 33
MoleculeChainsLengthOrganismImage
E-site tRNAg74Plasmodium falciparum 3D7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
34G
Query on 34G

Download CCD File 
P
emetine
C29 H40 N2 O4
AUVVAXYIELKVAI-TXQMCKRASA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
T
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1053801, APP1024678

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence