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: 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3a262Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SA263Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3221Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9189Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4261Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5272Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6306Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5195Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7194Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15A130Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8218Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16144Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20e118Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10137Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11151Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23145Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12141Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18156Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2954Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15151Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11161Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17137Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19145Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19170Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2182Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24AA [auth a]133Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25BA [auth b]105Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26CA [auth c]107Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27DA [auth d]82Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28eEA [auth e]67Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30FA [auth f]58Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNA2,092Plasmodium falciparum 3D7
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Entity ID: 33
MoleculeChains LengthOrganismImage
E-site tRNAGA [auth g]74Plasmodium falciparum 3D7
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
34G
Query on 34G

Download Ideal Coordinates CCD File 
WC [auth P]emetine
C29 H40 N2 O4
AUVVAXYIELKVAI-TXQMCKRASA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
XC [auth T]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth A]
BB [auth A]
BC [auth A]
CB [auth A]
AB [auth A],
AC [auth A],
BB [auth A],
BC [auth A],
CB [auth A],
CC [auth A],
DB [auth A],
DC [auth A],
EB [auth A],
EC [auth A],
FB [auth A],
FC [auth A],
GB [auth A],
GC [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
WA [auth A],
WB [auth A],
XA [auth A],
XB [auth A],
YA [auth A],
YB [auth A],
ZA [auth A],
ZB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC

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  (Full details and data files)

  • 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