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: 3.20 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
  • Structures With Same Primary Citation

  • 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

    Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL2
D
260Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0516900
Find proteins for Q8I3T9 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I3T9

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL3
E
386Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1027800
Find proteins for Q8IJC6 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IJC6

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL4
F
411Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0507100
Find proteins for Q8I431 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I431

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL5
G
173Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719600
Find proteins for Q8IBQ6 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IBQ6

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL6
H
190Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323100
Find proteins for Q8IE85 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IE85

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL6
I
221Plasmodium falciparum 3D7Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL8
J
283Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424400
Find proteins for Q8ILL2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL13
K
202Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1004000
Find proteins for Q8IJZ7 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL13
L
215Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0814000
Find proteins for Q8IAX6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL14
M
139Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1331800
Find proteins for Q8IE09 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL14
N
165Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1431700
Find proteins for Q8ILE8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL15
O
148Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0618300
Find proteins for C6KT23 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL15
P
205Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0415900
Find proteins for C0H4A6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL16
Q
219Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1414300
Find proteins for Q8ILV2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL18
R
294Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424100
Find proteins for Q8ILL3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL18
S
187Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341300
Find proteins for C0H5G3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL19
T
182Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0614500
Find proteins for C6KSY6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL22
W
203Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1351400
Find proteins for Q8IDI5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL22
X
139Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0821700
Find proteins for Q8IB51 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL23
Y
190Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323400
Find proteins for Q8IE82 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL24
0
162Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1309100
Find proteins for Q8IEM3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL27
1
146Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460700
Find proteins for Q8IKM5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL28
2
127Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142500
Find proteins for Q8IHU0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL29
3
124Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1124900
Find proteins for Q8IIB4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL29
4
67Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460300
Find proteins for C6S3J6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL30
5
257Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0307200
Find proteins for O97250 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL30
6
108Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1019400
Find proteins for Q8IJK8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL31
7
120Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0503800
Find proteins for Q8I463 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL32
8
131Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0903900
Find proteins for Q8I3B0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL33
9
140Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142600
Find proteins for Q8IHT9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL36
b
112Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1109900
Find proteins for Q8I713 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL37
c
92Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0706400
Find proteins for C0H4L5 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C0H4L5

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL38
d
87Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1130100
Find proteins for Q8II62 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL39
e
51Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0611700
Find proteins for C0H4H3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C0H4H3

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL40
f
128Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1365900
Find proteins for Q8ID50 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL43
h
96Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL37APFB0455w
Find proteins for O96184 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL44
i
104Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL44MAL3P2.9PFC0200W
Find proteins for O97231 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  O97231

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL20
U
184Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341200
Find proteins for Q8IDS6 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IDS6

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL21
V
161Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1426000
Find proteins for Q8ILK3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8ILK3

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein uL24
Z
126Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0312800
Find proteins for O77364 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  O77364

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL34
a
150Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0710600
Find proteins for Q8IBY4 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IBY4

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein eL41
g
39Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144300
Find proteins for C6S3G4 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C6S3G4

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Entity ID: 1
MoleculeChainsLengthOrganism
28S ribosomal RNAA3788Plasmodium falciparum 3D7

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAB119Plasmodium falciparum 3D7

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

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2014-12-17
    Changes: Other
  • Version 1.3: 2015-06-03
    Changes: Database references
  • Version 1.4: 2018-07-18
    Changes: Data collection