5UMD

Structure of the Plasmodium falciparum 80S ribosome bound to the antimalarial drug mefloquine

  • Classification: RIBOSOME
  • Organism(s): Plasmodium falciparum 3D7
  • Mutation(s): No 

  • Deposited: 2017-01-27 Released: 2017-03-01 
  • Deposition Author(s): Wong, W., Bai, X.-C., Brown, A., Scheres, S., Baum, J.
  • Funding Organization(s): NHMRC, Medical Research Council (United Kingdom), Wellcome Trust, Human Frontier Science Program, Department of Industry, Innovation, Science, Research and Tertiary Education, Australian Government|Australian Research Council

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

Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis.

Wong, W.Bai, X.C.Sleebs, B.E.Triglia, T.Brown, A.Thompson, J.K.Jackson, K.E.Hanssen, E.Marapana, D.S.Fernandez, I.S.Ralph, S.A.Cowman, A.F.Scheres, S.H.Baum, J.

(2017) Nat Microbiol 2: 17031-17031

  • DOI: 10.1038/nmicrobiol.2017.31
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, is critical to the development of their second-gener ...

    Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, is critical to the development of their second-generation derivatives to improve drug potency towards inhibition of their molecular targets. Mefloquine is a widely used antimalarial without a known mode of action. Here, we demonstrate that mefloquine is a protein synthesis inhibitor. We solved a 3.2 Å cryo-electron microscopy structure of the Plasmodium falciparum 80S ribosome with the (+)-mefloquine enantiomer bound to the ribosome GTPase-associated centre. Mutagenesis of mefloquine-binding residues generates parasites with increased resistance, confirming the parasite-killing mechanism. Furthermore, structure-guided derivatives with an altered piperidine group, predicted to improve binding, show enhanced parasiticidal effect. These data reveal one possible mode of action for mefloquine and demonstrate the vast potential of cryo-electron microscopy to guide the development of mefloquine derivatives to inhibit parasite protein synthesis.


    Organizational Affiliation

    Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK.



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4F411Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0507100
Find proteins for Q8I431 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15P205Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0415900
Find proteins for C0H4A6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5, putativeR294Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424100
Find proteins for Q8ILL3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23Y190Plasmodium 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 L24, putative0162Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1309100
Find proteins for Q8IEM3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L282127Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142500
Find proteins for Q8IHU0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L317120Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0503800
Find proteins for Q8I463 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37c92Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0706400
Find proteins for C0H4L5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40f128Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1365900
Find proteins for Q8ID50 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41g39Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144300
Find proteins for C6S3G4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L44i104Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL44MAL3P2.9PFC0200W
Find proteins for O97231 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-3, putativeJ283Plasmodium 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 L13, putativeK202Plasmodium 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 L13L215Plasmodium 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 L23, putativeM139Plasmodium 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 L14, putativeN165Plasmodium 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 L27a, putativeO148Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0618300
Find proteins for C6KT23 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10, putativeQ219Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1414300
Find proteins for Q8ILV2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-2, putativeS187Plasmodium 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 L19T182Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0614500
Find proteins for C6KSY6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18aU184Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341200
Find proteins for Q8IDS6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21V161Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1426000
Find proteins for Q8ILK3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17, putativeW203Plasmodium 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 L22, putativeX139Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0821700
Find proteins for Q8IB51 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26, putativeZ126Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0312800
Find proteins for O77364 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L271146Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460700
Find proteins for Q8IKM5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35, putative3124Plasmodium 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 L29, putative467Plasmodium 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 L7, putative5257Plasmodium 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 L30e, putative6108Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1019400
Find proteins for Q8IJK8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L328131Plasmodium 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 L35Ae, putative9140Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142600
Find proteins for Q8IHT9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34a150Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0710600
Find proteins for Q8IBY4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36b112Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1109900
Find proteins for Q8I713 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2D260Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0516900
Find proteins for Q8I3T9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38d87Plasmodium 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 L39e51Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0611700
Find proteins for C0H4H3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37ah96Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL37APFB0455w
Find proteins for O96184 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3E386Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1027800
Find proteins for Q8IJC6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11a, putativeG173Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719600
Find proteins for Q8IBQ6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6, putativeH190Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323100
Find proteins for Q8IE85 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-2, putativeI221Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAB119Plasmodium falciparum 3D7

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

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNAC159Plasmodium falciparum 3D7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YMZ
Query on YMZ

Download CCD File 
A, K
Mefloquine
C17 H16 F6 N2 O
XEEQGYMUWCZPDN-SWLSCSKDSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, B, C, M
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

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NHMRCAustraliaAPP1024678
NHMRCAustraliaAPP1053801
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1013
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
Wellcome TrustUnited Kingdom100993/Z/13/Z
Human Frontier Science ProgramUnited KingdomRGY0071/2011
Department of Industry, Innovation, Science, Research and Tertiary Education, Australian Government|Australian Research CouncilAustraliaFT100100112

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Advisory, Derived calculations, Other