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 3J7A | pdb_00003j7a

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: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 1,263.06 kDa 
  • Atom Count: 68,866 
  • Modeled Residue Count: 5,788 
  • Deposited Residue Count: 7,121 
  • Unique protein chains: 31
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS1262Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for O97313 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS2263Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IJD4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS3221Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS4189Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS4261Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS5272Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS6306Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS7195Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS7194Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS8130Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS8218Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS9144Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS10118Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS10137Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS11151Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for A0A5K1K925 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS12145Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS12141Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for O97249 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS13156Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS1454Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS15151Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS17161Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS17137Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein uS19145Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS19170Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS2182Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS24AA [auth 1]133Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS25BA [auth 2]105Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS26CA [auth 3]107Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS27DA [auth 4]82Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS28EA [auth 5]67Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein eS30FA [auth 6]58Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for O96269 (Plasmodium falciparum (isolate 3D7))
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNA2,092Plasmodium falciparum 3D7
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Entity ID: 33
MoleculeChains LengthOrganismImage
tRNAGA [auth 7]74Plasmodium falciparum 3D7
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
34G

Query on 34G



Download:Ideal Coordinates CCD File
PC [auth A]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],
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],
WC [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: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Structure summary
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary