6AZ1

Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.

Shalev-Benami, M.Zhang, Y.Rozenberg, H.Nobe, Y.Taoka, M.Matzov, D.Zimmerman, E.Bashan, A.Isobe, T.Jaffe, C.L.Yonath, A.Skiniotis, G.

(2017) Nat Commun 8: 1589-1589

  • DOI: 10.1038/s41467-017-01664-4
  • Primary Citation of Related Structures:  
    6AZ1, 6AZ3

  • PubMed Abstract: 
  • Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL) ...

    Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL). The structure reveals the mechanism by which the drug induces its deleterious effects on the parasite. We further show that PAR interferes with several aspects of cytosolic translation, thus highlighting the cytosolic rather than the mitochondrial ribosome as the primary drug target. The results also highlight unique as well as conserved elements in the PAR-binding pocket that can serve as hotspots for the development of novel therapeutics.


    Organizational Affiliation

    Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. yiorgo@stanford.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein s1eA264Leishmania donovaniMutation(s): 0 
Find proteins for E9BRS2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S2B246Leishmania donovaniMutation(s): 0 
Find proteins for A4IDS4 (Leishmania infantum)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S4D190Leishmania donovaniMutation(s): 0 
Find proteins for E9BTJ0 (Leishmania donovani (strain BPK282A1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S4eE273Leishmania donovaniMutation(s): 0 
Find proteins for E9BBI6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S5F265Leishmania donovaniMutation(s): 0 
Find proteins for E9BNF0 (Leishmania donovani (strain BPK282A1))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S6eG249Leishmania donovaniMutation(s): 0 
Find proteins for O44012 (Leishmania infantum)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S7H190Leishmania donovaniMutation(s): 0 
Find proteins for A0A381MCG8 (Leishmania infantum)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S8J130Leishmania donovaniMutation(s): 0 
Find proteins for E9BAV6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S8eK220Leishmania donovaniMutation(s): 0 
Find proteins for E9BH78 (Leishmania donovani (strain BPK282A1))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S9L149Leishmania donovaniMutation(s): 0 
Find proteins for E9BI96 (Leishmania donovani (strain BPK282A1))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S10M116Leishmania donovaniMutation(s): 0 
Find proteins for E9BJI2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S10eN153Leishmania donovaniMutation(s): 0 
Find proteins for E9BTG4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S11O144Leishmania donovaniMutation(s): 0 
Find proteins for E9BMA8 (Leishmania donovani (strain BPK282A1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S12P143Leishmania donovaniMutation(s): 0 
Find proteins for E9BFB6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S12eQ141Leishmania donovaniMutation(s): 0 
Find proteins for E9BBC0 (Leishmania donovani (strain BPK282A1))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S13R153Leishmania donovaniMutation(s): 0 
Find proteins for E9BTF9 (Leishmania donovani (strain BPK282A1))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S14S57Leishmania donovaniMutation(s): 0 
Find proteins for E9BJV7 (Leishmania donovani (strain BPK282A1))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S17U173Leishmania donovaniMutation(s): 0 
Gene Names: LdCL_200021000LdCL_210023700
Find proteins for Q9TXA6 (Leishmania donovani)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S19W152Leishmania donovaniMutation(s): 0 
Find proteins for E9BFQ0 (Leishmania donovani (strain BPK282A1))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S19eX179Leishmania donovaniMutation(s): 0 
Find proteins for E9BR60 (Leishmania donovani (strain BPK282A1))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S21eY159Leishmania donovaniMutation(s): 0 
Find proteins for E9BAR6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S24eZ137Leishmania donovaniMutation(s): 0 
Find proteins for E9BU11 (Leishmania donovani (strain BPK282A1))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S25ea120Leishmania donovaniMutation(s): 0 
Find proteins for E9BHM6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S26eb112Leishmania donovaniMutation(s): 0 
Find proteins for E9BK95 (Leishmania donovani (strain BPK282A1))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S27ec86Leishmania donovaniMutation(s): 0 
Find proteins for E9BUA2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S28ed87Leishmania donovaniMutation(s): 0 
Find proteins for E9BIH3 (Leishmania donovani (strain BPK282A1))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S30ee66Leishmania donovaniMutation(s): 0 
Find proteins for E9BLG3 (Leishmania donovani (strain BPK282A1))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S31ef152Leishmania donovaniMutation(s): 0 
Find proteins for E9BTC5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
LACK1g312Leishmania donovaniMutation(s): 0 
Find proteins for Q9BIJ5 (Leishmania donovani)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S15T151Leishmania donovaniMutation(s): 0 
Find proteins for E9BPR7 (Leishmania donovani (strain BPK282A1))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S17eV143Leishmania donovaniMutation(s): 0 
Find proteins for E9BJZ5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S3C219Leishmania donovaniMutation(s): 0 
Find proteins for E9BQ25 (Leishmania donovani (strain BPK282A1))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S7eI200Leishmania donovaniMutation(s): 0 
Find proteins for E9B7A8 (Leishmania donovani (strain BPK282A1))
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Entity ID: 34
MoleculeChainsLengthOrganismImage
ribosomal RNA 18S12203Leishmania donovani
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Entity ID: 35
MoleculeChainsLengthOrganismImage
tRNA-Phe276Escherichia coli
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Entity ID: 36
MoleculeChainsLengthOrganismImage
P-site tRNA377Escherichia coli
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Entity ID: 37
MoleculeChainsLengthOrganismImage
E-site tRNA476Escherichia coli
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  • Entity ID: 38
    MoleculeChainsLengthOrganismImage
    mRNA513Leishmania donovani
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PAR
    Query on PAR

    Download CCD File 
    1
    PAROMOMYCIN
    C23 H45 N5 O14
    UOZODPSAJZTQNH-LSWIJEOBSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    1, 5, C, D, S
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.70 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2017-12-06
      Type: Initial release
    • Version 1.1: 2017-12-13
      Changes: Database references
    • Version 2.0: 2019-07-03
      Changes: Data collection, Non-polymer description, Structure summary