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

wwPDB Validation 3D Report Full Report


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

  • 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: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL2
D
260Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I3T9 (Plasmodium falciparum)
Go to UniProtKB:  Q8I3T9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL3
E
386Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IJC6 (Plasmodium falciparum)
Go to UniProtKB:  Q8IJC6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL4
F
411Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I431 (Plasmodium falciparum)
Go to UniProtKB:  Q8I431
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL5
G
173Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IBQ6 (Plasmodium falciparum)
Go to UniProtKB:  Q8IBQ6
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL6
H
190Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IE85 (Plasmodium falciparum)
Go to UniProtKB:  Q8IE85
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL6
I
221Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IDV1 (Plasmodium falciparum)
Go to UniProtKB:  Q8IDV1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL8
J
283Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILL2 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILL2
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL13
K
202Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IJZ7 (Plasmodium falciparum)
Go to UniProtKB:  Q8IJZ7
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL13
L
215Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IAX6 (Plasmodium falciparum)
Go to UniProtKB:  Q8IAX6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL14
M
139Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IE09 (Plasmodium falciparum)
Go to UniProtKB:  Q8IE09
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL14
N
165Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILE8 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILE8
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL15
O
148Plasmodium falciparumMutation(s): 0 
Find proteins for C6KT23 (Plasmodium falciparum)
Go to UniProtKB:  C6KT23
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL15
P
205Plasmodium falciparumMutation(s): 0 
Find proteins for C0H4A6 (Plasmodium falciparum)
Go to UniProtKB:  C0H4A6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL16
Q
219Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILV2 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILV2
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL18
R
294Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILL3 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILL3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL18
S
187Plasmodium falciparumMutation(s): 0 
Find proteins for C0H5G3 (Plasmodium falciparum)
Go to UniProtKB:  C0H5G3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL19
T
182Plasmodium falciparumMutation(s): 0 
Find proteins for C6KSY6 (Plasmodium falciparum)
Go to UniProtKB:  C6KSY6
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL20
U
184Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IDS6 (Plasmodium falciparum)
Go to UniProtKB:  Q8IDS6
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL21
V
161Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ILK3 (Plasmodium falciparum)
Go to UniProtKB:  Q8ILK3
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL22
W
203Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IDI5 (Plasmodium falciparum)
Go to UniProtKB:  Q8IDI5
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL22
X
139Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IB51 (Plasmodium falciparum)
Go to UniProtKB:  Q8IB51
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL23
Y
190Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IE82 (Plasmodium falciparum)
Go to UniProtKB:  Q8IE82
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL24
Z
126Plasmodium falciparumMutation(s): 0 
Find proteins for O77364 (Plasmodium falciparum)
Go to UniProtKB:  O77364
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL24
0
162Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IEM3 (Plasmodium falciparum)
Go to UniProtKB:  Q8IEM3
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL27
1
146Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IKM5 (Plasmodium falciparum)
Go to UniProtKB:  Q8IKM5
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL28
2
127Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IHU0 (Plasmodium falciparum)
Go to UniProtKB:  Q8IHU0
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL29
3
124Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IIB4 (Plasmodium falciparum)
Go to UniProtKB:  Q8IIB4
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL29
4
67Plasmodium falciparumMutation(s): 0 
Find proteins for C6S3J6 (Plasmodium falciparum)
Go to UniProtKB:  C6S3J6
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL30
5
257Plasmodium falciparumMutation(s): 0 
Find proteins for O97250 (Plasmodium falciparum)
Go to UniProtKB:  O97250
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL30
6
108Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IJK8 (Plasmodium falciparum)
Go to UniProtKB:  Q8IJK8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL31
7
120Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I463 (Plasmodium falciparum)
Go to UniProtKB:  Q8I463
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL32
8
131Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I3B0 (Plasmodium falciparum)
Go to UniProtKB:  Q8I3B0
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL33
9
140Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IHT9 (Plasmodium falciparum)
Go to UniProtKB:  Q8IHT9
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL34
a
150Plasmodium falciparumMutation(s): 0 
Find proteins for Q8IBY4 (Plasmodium falciparum)
Go to UniProtKB:  Q8IBY4
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL36
b
112Plasmodium falciparumMutation(s): 0 
Find proteins for Q8I713 (Plasmodium falciparum)
Go to UniProtKB:  Q8I713
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL37
c
92Plasmodium falciparumMutation(s): 0 
Find proteins for C0H4L5 (Plasmodium falciparum)
Go to UniProtKB:  C0H4L5
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL38
d
87Plasmodium falciparumMutation(s): 0 
Find proteins for Q8II62 (Plasmodium falciparum)
Go to UniProtKB:  Q8II62
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL39
e
51Plasmodium falciparumMutation(s): 0 
Find proteins for C0H4H3 (Plasmodium falciparum)
Go to UniProtKB:  C0H4H3
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL40
f
128Plasmodium falciparumMutation(s): 0 
Find proteins for Q8ID50 (Plasmodium falciparum)
Go to UniProtKB:  Q8ID50
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL41
g
39Plasmodium falciparumMutation(s): 0 
Find proteins for C6S3G4 (Plasmodium falciparum)
Go to UniProtKB:  C6S3G4
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL43
h
96Plasmodium falciparumMutation(s): 0 
Gene Names: RPL37A
Find proteins for O96184 (Plasmodium falciparum)
Go to Gene View: RPL37A
Go to UniProtKB:  O96184
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL44
i
104Plasmodium falciparumMutation(s): 0 
Gene Names: RPL44
Find proteins for O97231 (Plasmodium falciparum)
Go to UniProtKB:  O97231
Entity ID: 1
MoleculeChainsLengthOrganism
28S ribosomal RNAA3788Plasmodium falciparum 3D7
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAB119Plasmodium falciparum 3D7
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNAC159Plasmodium falciparum 3D7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
a, c, f, h, i
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, M, Q
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-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: 2014-12-10
    Type: Other
  • Version 1.2: 2014-12-17
    Type: Other
  • Version 1.3: 2015-06-03
    Type: Database references
  • Version 1.4: 2018-07-18
    Type: Data collection