6AZ1

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.7 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
  • Primary Citation of Related Structures:  

  • 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 resoluti ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein s1e
A
264Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRS2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRS2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S2
B
246Leishmania infantumMutation(s): 0 
Find proteins for A4IDS4 (Leishmania infantum)
Go to UniProtKB:  A4IDS4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S3
C
219Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BQ25 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BQ25
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S4
D
190Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BTJ0 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BTJ0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S4e
E
273Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BBI6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BBI6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S5
F
265Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BNF0 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BNF0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S6e
G
249Leishmania infantumMutation(s): 0 
Gene Names: RPS6 (RS6)
Find proteins for O44012 (Leishmania infantum)
Go to Gene View: RPS6
Go to UniProtKB:  O44012
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S7
H
190Leishmania infantumMutation(s): 0 
Find proteins for A0A381MCG8 (Leishmania infantum)
Go to UniProtKB:  A0A381MCG8
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S7e
I
200Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B7A8 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B7A8
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S8
J
130Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BAV6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BAV6
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S8e
K
220Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BH78 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BH78
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S9
L
149Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BI96 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BI96
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S10
M
116Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BJI2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BJI2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S10e
N
153Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BTG4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BTG4
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S11
O
144Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BMA8 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMA8
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S12
P
143Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFB6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFB6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S12e
Q
141Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BBC0 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BBC0
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S13
R
153Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BTF9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BTF9
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S14
S
57Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BJV7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BJV7
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S15
T
151Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BPR7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BPR7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S17
U
173Leishmania donovaniMutation(s): 0 
Find proteins for Q9TXA6 (Leishmania donovani)
Go to UniProtKB:  Q9TXA6
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S17e
V
143Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BJZ5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BJZ5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S19
W
152Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFQ0 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFQ0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S19e
X
179Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BR60 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BR60
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S21e
Y
159Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BAR6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BAR6
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S24e
Z
137Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BU11 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU11
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S25e
a
120Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BHM6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BHM6
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S26e
b
112Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BK95 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BK95
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S27e
c
86Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BUA2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUA2
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S28e
d
87Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BIH3 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BIH3
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S30e
e
66Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BLG3 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BLG3
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein S31e
f
152Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BTC5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BTC5
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
LACK1
g
312Leishmania donovaniMutation(s): 0 
Find proteins for Q9BIJ5 (Leishmania donovani)
Go to UniProtKB:  Q9BIJ5
Entity ID: 34
MoleculeChainsLengthOrganism
ribosomal RNA 18S12203Leishmania donovani
Entity ID: 35
MoleculeChainsLengthOrganism
tRNA-Phe276Escherichia coli
Entity ID: 36
MoleculeChainsLengthOrganism
P-site tRNA377Escherichia coli
Entity ID: 37
MoleculeChainsLengthOrganism
E-site tRNA476Escherichia coli
Entity ID: 38
MoleculeChainsLengthOrganism
mRNA513Leishmania donovani
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download SDF File 
Download CCD File 
1
PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
1, 5, C, D, S
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
1
RNA LINKINGC11 H16 N5 O7 PA
5MC
Query on 5MC
1
RNA LINKINGC10 H16 N3 O8 PC
OMU
Query on OMU
1
RNA LINKINGC10 H15 N2 O9 PU
C4J
Query on C4J
1
RNA linkingC14 H22 N3 O11 P

--

OMC
Query on OMC
1
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
1
RNA LINKINGC12 H18 N5 O7 PA
MIA
Query on MIA
2
RNA LINKINGC16 H26 N5 O7 P SA
M1Y
Query on M1Y
1
RNA linkingC10 H15 N2 O9 P

--

OMG
Query on OMG
1
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
1
RNA LINKINGC11 H18 N5 O8 PG
4OC
Query on 4OC
1
RNA LINKINGC11 H18 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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