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


This is version 2.0 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: https://doi.org/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). 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

    Faculty of Chemistry, Department of Structural Biology, Weizmann Institute of Science, Rehovot, 761001, Israel. moransb@stanford.edu.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein s1e264Leishmania donovaniMutation(s): 0 
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Find proteins for E9BRS2 (Leishmania donovani)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S2246Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A4IDS4 (Leishmania infantum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S3219Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S4190Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S5H5Z2 (Leishmania donovani)
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UniProt GroupA0A3S5H5Z2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S4e273Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S5265Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S6e249Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S7190Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S7e200Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S8130Leishmania donovaniMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S8e220Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S9149Leishmania donovaniMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S10116Leishmania donovaniMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S10e153Leishmania donovaniMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S11144Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S7X3Z7 (Leishmania donovani)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S12143Leishmania donovaniMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S12e141Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S5H6N5 (Leishmania donovani)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S13153Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for E9BTF9 (Leishmania donovani)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S1457Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S15151Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S7X790 (Leishmania donovani)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S17173Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for Q9TXA6 (Leishmania donovani)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S17e143Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S19152Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S19e179Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for E9BR60 (Leishmania donovani)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S21e159Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for E9BAR6 (Leishmania donovani)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S24e137Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8IKW0 (Leishmania donovani)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S25eAA [auth a]120Leishmania donovaniMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S26eBA [auth b]112Leishmania donovaniMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S27eCA [auth c]86Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8ID11 (Leishmania donovani)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S28eDA [auth d]87Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S30eEA [auth e]66Leishmania donovaniMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S31eFA [auth f]152Leishmania donovaniMutation(s): 0 
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Find proteins for A0A3S7XAC2 (Leishmania donovani)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
LACK1GA [auth g]312Leishmania donovaniMutation(s): 0 
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Entity ID: 34
MoleculeChains LengthOrganismImage
ribosomal RNA 18SHA [auth 1]2,203Leishmania donovani
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Entity ID: 35
MoleculeChains LengthOrganismImage
tRNA-PheIA [auth 2]76Escherichia coli
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Entity ID: 36
MoleculeChains LengthOrganismImage
P-site tRNAJA [auth 3]77Escherichia coli
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Entity ID: 37
MoleculeChains LengthOrganismImage
E-site tRNAKA [auth 4]76Escherichia coli
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Entity ID: 38
MoleculeChains LengthOrganismImage
mRNALA [auth 5]13Leishmania donovani
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
QA [auth 1]
RA [auth 1]
SA [auth 1]
TA [auth 1]
UA [auth 1]
QA [auth 1],
RA [auth 1],
SA [auth 1],
TA [auth 1],
UA [auth 1],
VA [auth 1]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 1]
BB [auth 1]
CB [auth 1]
DB [auth 1]
EB [auth 1]
AB [auth 1],
BB [auth 1],
CB [auth 1],
DB [auth 1],
EB [auth 1],
FB [auth 1],
GB [auth 1],
HB [auth 1],
IB [auth 1],
JB [auth 1],
KB [auth 1],
LB [auth 1],
MA [auth C],
MB [auth 1],
NA [auth D],
NB [auth 1],
OA [auth S],
OB [auth 1],
PA [auth 1],
PB [auth 5],
WA [auth 1],
XA [auth 1],
YA [auth 1],
ZA [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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