6AZ3

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.5 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. ada.yonath@weizmann.ac.il.,Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. yiorgo@stanford.edu.,Faculty of Chemistry, Department of Structural Biology, Weizmann Institute of Science, Rehovot, 761001, Israel. moransb@stanford.edu.,Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo, 192-0397, Japan.,Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Faculty of Chemistry, Department of Structural Biology, Weizmann Institute of Science, Rehovot, 761001, Israel.,Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.,Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. moransb@stanford.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL2
A
254N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL3
B
402N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL4
C
366Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BKR3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL5
D
168Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFL1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL6
E
186Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFB5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL6
F
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL8
G
348Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B949
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL13
H
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL13
I
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL14
J
134Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ4
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL14
K
149Leishmania donovaniMutation(s): 0 
Gene Names: RPL14 (LPD23)
Find proteins for Q25278 (Leishmania donovani)
Go to Gene View: RPL14
Go to UniProtKB:  Q25278
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL15
L
144Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSQ2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ2
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL15
M
203Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BMB4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMB4
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL16
N
213Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B840
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL18
O
305Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BS61
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL18
P
197Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUI1
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL19
Q
189Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8Q2
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL20
R
178Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRT7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL21
S
154Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRE2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL22
T
154Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BGL6
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL22
U
121Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU52
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL23
V
118Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B8R9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8R9
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL24
W
121N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL24
X
65N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL27
Y
132Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BP34
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL28
Z
140Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BAU9
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL29
a
125Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BIP6
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL29
b
68Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BU64 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU64
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL30
c
227Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BI29
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL30
d
92Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRQ6
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL31
e
119Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSK4
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL32
f
130Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFJ5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFJ5
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL33
g
125Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BR22
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL34
h
125Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BUA1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUA1
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL36
i
97Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BF65 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BF65
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL37
j
80Leishmania donovaniMutation(s): 0 
Gene Names: RPL37
Find proteins for P62885 (Leishmania donovani)
Go to Gene View: RPL37
Go to UniProtKB:  P62885
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL38
k
76Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B7P2
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL39
l
50Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BCX6
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL40
m
50Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BMW6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMW6
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL41
n
33N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL43
o
90Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFK4
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL44
p
96Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BBL5
Entity ID: 43
MoleculeChainsLengthOrganism
rRNA alpha11778Leishmania donovani
Entity ID: 44
MoleculeChainsLengthOrganism
rRNA beta21526Leishmania donovani
Entity ID: 45
MoleculeChainsLengthOrganism
rRNA gamma3211Leishmania donovani
Entity ID: 46
MoleculeChainsLengthOrganism
rRNA delta4183Leishmania donovani
Entity ID: 47
MoleculeChainsLengthOrganism
rRNA epsilon5133Leishmania donovani
Entity ID: 48
MoleculeChainsLengthOrganism
rRNA zeta671Leishmania donovani
Entity ID: 49
MoleculeChainsLengthOrganism
rRNA 5.8S7171Leishmania donovani
Entity ID: 50
MoleculeChainsLengthOrganism
rRNA 5S8118Leishmania donovani
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download SDF File 
Download CCD File 
1, 2, 7
PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
C
Query on C

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

Download SDF File 
Download CCD File 
1, 2, 3, 4, 5, 7
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
1, 2, 7
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
1, 2, 3, 7
RNA LINKINGC10 H15 N2 O9 PU
OMC
Query on OMC
1, 2
RNA LINKINGC10 H16 N3 O8 PC
OMG
Query on OMG
1, 2, 4, 7
RNA LINKINGC11 H16 N5 O8 PG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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