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

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    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 ...

    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 eS1B262Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: MAL3P7.35PFC1020c
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS2C263Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF10_0264
UniProt
Find proteins for Q8IJD4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS3D221Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1465900
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS4E189Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0520000
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Find proteins for Q8I3R0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS4F261Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1105400
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS5G272Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1447000
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS6H306Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1342000
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Entity ID: 9
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40S ribosomal protein uS7I195Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0721600
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Entity ID: 10
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40S ribosomal protein eS7J194Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1302800
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS8K130Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0316800
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Find proteins for O77395 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 12
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40S ribosomal protein eS8L218Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1408600
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Find proteins for Q8IM10 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS9M144Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0813900
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Entity ID: 14
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40S ribosomal protein uS10N118Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1003500
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Entity ID: 15
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40S ribosomal protein eS10O137Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719700
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Entity ID: 16
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40S ribosomal protein uS11P151Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 17
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40S ribosomal protein uS12Q145Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0306900
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Find proteins for O97248 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS12R141Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPS12MAL3P2.28PFC0295C
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS13S156Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1126200
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Find proteins for Q8IIA2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 20
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40S ribosomal protein uS14T54Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0705700
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS15U151Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1358800
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS17V161Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0317600
UniProt
Find proteins for O77381 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS17W137Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1242700
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Find proteins for Q8I502 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS19X145Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1317800
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS19Y170Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0422400
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS21Z82Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144000
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS24AA [auth 1]133Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0519400
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS25BA [auth 2]105Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1421200
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS26CA [auth 3]107Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0217800
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS27DA [auth 4]82Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1308300
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Find proteins for Q8IEN2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS28EA [auth 5]67Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1461300
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS30FA [auth 6]58Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPS30PFB0885w
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA2,092Plasmodium falciparum 3D7
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Entity ID: 33
MoleculeChainsLengthOrganismImage
tRNAGA [auth 7]74Plasmodium falciparum 3D7
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Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
XC [auth T]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
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

View Full Validation Report



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