6AZ3

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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
  • Structures With Same Primary Citation

  • 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 LengthOrganismDetails
ribosomal protein uL2A254Leishmania donovaniMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL3B402Leishmania donovaniMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL4C366Leishmania donovaniMutation(s): 0 
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL6F195Leishmania donovaniMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL8G348Leishmania donovaniMutation(s): 0 
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL13H221Leishmania donovaniMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL13I212Leishmania donovaniMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL14J134Leishmania donovaniMutation(s): 0 
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL14K149Leishmania donovaniMutation(s): 0 
Gene Names: RPL14LPD23
Find proteins for Q25278 (Leishmania donovani)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL15L144Leishmania donovaniMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL15M203Leishmania donovaniMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL16N213Leishmania donovaniMutation(s): 0 
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL18O305Leishmania donovaniMutation(s): 0 
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL18P197Leishmania donovaniMutation(s): 0 
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL20R178Leishmania donovaniMutation(s): 0 
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL21S154Leishmania donovaniMutation(s): 0 
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL22T154Leishmania donovaniMutation(s): 0 
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL22U121Leishmania donovaniMutation(s): 0 
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL23V118Leishmania donovaniMutation(s): 0 
Find proteins for E9B8R9 (Leishmania donovani (strain BPK282A1))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL24W121Leishmania donovaniMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL27Y132Leishmania donovaniMutation(s): 0 
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL28Z140Leishmania donovaniMutation(s): 0 
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL29a125Leishmania donovaniMutation(s): 0 
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL30c227Leishmania donovaniMutation(s): 0 
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL30d92Leishmania donovaniMutation(s): 0 
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL31e119Leishmania donovaniMutation(s): 0 
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL32f130Leishmania donovaniMutation(s): 0 
Find proteins for E9BFJ5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL34h125Leishmania donovaniMutation(s): 0 
Find proteins for E9BUA1 (Leishmania donovani (strain BPK282A1))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL36i97Leishmania donovaniMutation(s): 0 
Find proteins for E9BF65 (Leishmania donovani (strain BPK282A1))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL37j80Leishmania donovaniMutation(s): 0 
Gene Names: RPL37
Find proteins for P62885 (Leishmania donovani)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL38k76Leishmania donovaniMutation(s): 0 
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL39l50Leishmania donovaniMutation(s): 0 
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL41n33Leishmania donovaniMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL43o90Leishmania donovaniMutation(s): 0 
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL44p96Leishmania donovaniMutation(s): 0 
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL19Q189Leishmania donovaniMutation(s): 0 
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL24X65Leishmania donovaniMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL29b68Leishmania donovaniMutation(s): 0 
Find proteins for E9BU64 (Leishmania donovani (strain BPK282A1))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL33g125Leishmania donovaniMutation(s): 0 
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL40m50Leishmania donovaniMutation(s): 0 
Find proteins for E9BMW6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL5D168Leishmania donovaniMutation(s): 0 
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL6E186Leishmania donovaniMutation(s): 0 
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 43
MoleculeChainsLengthOrganism
rRNA alpha11778Leishmania donovani

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Entity ID: 44
MoleculeChainsLengthOrganism
rRNA beta21526Leishmania donovani

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Entity ID: 45
MoleculeChainsLengthOrganism
rRNA gamma3211Leishmania donovani

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Entity ID: 46
MoleculeChainsLengthOrganism
rRNA delta4183Leishmania donovani

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Entity ID: 47
MoleculeChainsLengthOrganism
rRNA epsilon5133Leishmania donovani

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Entity ID: 48
MoleculeChainsLengthOrganism
rRNA zeta671Leishmania donovani

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Entity ID: 49
MoleculeChainsLengthOrganism
rRNA 5.8S7171Leishmania donovani

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Entity ID: 50
MoleculeChainsLengthOrganism
rRNA 5S8118Leishmania donovani
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

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1, 2, 7
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
C
Query on C

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2
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

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1, 2, 3, 4, 5, 7
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references