3J7A

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: 3.2 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: e03080-e03080

  • DOI: 10.7554/eLife.03080
  • Primary Citation of Related Structures:  1VX6, 1VX7, 3J79
  • Also Cited By: 3JBN, 3JBO, 3JBP

  • 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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS1
B
262Plasmodium falciparumN/A
Find proteins for O97313 (Plasmodium falciparum)
Go to UniProtKB:  O97313
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS2
C
263Plasmodium falciparumN/A
Find proteins for Q8IJD4 (Plasmodium falciparum)
Go to UniProtKB:  Q8IJD4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS3
D
221Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IKH8 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IKH8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS4
E
189Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8I3R0 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I3R0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS4
F
261Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IIU8 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IIU8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS5
G
272Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IL02 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IL02
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS6
H
306Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IDR9 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IDR9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS7
I
195Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IBN5 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IBN5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS7
J
194Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IET7 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IET7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS8
K
130Plasmodium falciparum (isolate 3D7)N/A
Find proteins for O77395 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  O77395
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS8
L
218Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IM10 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IM10
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS9
M
144Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IAX5 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IAX5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS10
N
118Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IK02 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IK02
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS10
O
137Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IBQ5 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IBQ5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS11
P
151Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8I3U6 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I3U6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS12
Q
145Plasmodium falciparum (isolate 3D7)N/A
Find proteins for O97248 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  O97248
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS12
R
141Plasmodium falciparumGene Names: RPS12
Find proteins for O97249 (Plasmodium falciparum)
Go to Gene View: RPS12
Go to UniProtKB:  O97249
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS13
S
156Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IIA2 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IIA2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS14
T
54Plasmodium falciparum (isolate 3D7)N/A
Find proteins for C0H4K8 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C0H4K8
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS15
U
151Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IDB0 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IDB0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS17
V
161Plasmodium falciparum (isolate 3D7)N/A
Find proteins for O77381 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  O77381
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS17
W
137Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8I502 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I502
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS19
X
145Plasmodium falciparum (isolate 3D7)N/A
Find proteins for C0H5C2 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C0H5C2
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS19
Y
170Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IFP2 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IFP2
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS21
Z
82Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IHS5 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IHS5
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS24
1
133Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8I3R6 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I3R6
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS25
2
105Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8ILN8 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8ILN8
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS26
3
107Plasmodium falciparum (isolate 3D7)N/A
Find proteins for O96258 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  O96258
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS27
4
82Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IEN2 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IEN2
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS28
5
67Plasmodium falciparum (isolate 3D7)N/A
Find proteins for Q8IKL9 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IKL9
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS30
6
58Plasmodium falciparumGene Names: RPS30
Find proteins for O96269 (Plasmodium falciparum)
Go to UniProtKB:  O96269
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNAA2092Plasmodium falciparum 3D7
Entity ID: 33
MoleculeChainsLengthOrganism
tRNA774Plasmodium falciparum 3D7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
34G
Query on 34G

Download SDF File 
Download CCD File 
A
emetine
(3beta,14beta)-6',7',10,11-tetramethoxyemetan
C29 H40 N2 O4
AUVVAXYIELKVAI-TXQMCKRASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Structure summary
  • Version 1.2: 2015-06-03
    Type: Database references