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 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

    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 uL2
A
254Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL3
B
402Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL4
C
366Leishmania donovaniMutation(s): 0 
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BKR3

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL5
D
168Leishmania donovaniMutation(s): 0 
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFL1

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL6
E
186Leishmania donovaniMutation(s): 0 
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFB5

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL6
F
195Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL8
G
348Leishmania donovaniMutation(s): 0 
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B949

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL13
H
221Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL13
I
212Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL14
J
134Leishmania donovaniMutation(s): 0 
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ4

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL14
K
149Leishmania donovaniMutation(s): 0 
Gene Names: RPL14LPD23
Find proteins for Q25278 (Leishmania donovani)
Go to UniProtKB:  Q25278

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL15
L
144Leishmania donovaniMutation(s): 0 
Find proteins for E9BSQ2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ2

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL15
M
203Leishmania donovaniMutation(s): 0 
Find proteins for E9BMB4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMB4

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL16
N
213Leishmania donovaniMutation(s): 0 
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B840

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL18
O
305Leishmania donovaniMutation(s): 0 
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BS61

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL18
P
197Leishmania donovaniMutation(s): 0 
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUI1

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL19
Q
189Leishmania donovaniMutation(s): 0 
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8Q2

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL20
R
178Leishmania donovaniMutation(s): 0 
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRT7

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL21
S
154Leishmania donovaniMutation(s): 0 
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRE2

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL22
T
154Leishmania donovaniMutation(s): 0 
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BGL6

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL22
U
121Leishmania donovaniMutation(s): 0 
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU52

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL23
V
118Leishmania donovaniMutation(s): 0 
Find proteins for E9B8R9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8R9

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL24
W
121Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL24
X
65Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL27
Y
132Leishmania donovaniMutation(s): 0 
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BP34

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL28
Z
140Leishmania donovaniMutation(s): 0 
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL29
a
125Leishmania donovaniMutation(s): 0 
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL29
b
68Leishmania donovaniMutation(s): 0 
Find proteins for E9BU64 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU64

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uL30
c
227Leishmania donovaniMutation(s): 0 
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BI29

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL30
d
92Leishmania donovaniMutation(s): 0 
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRQ6

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL31
e
119Leishmania donovaniMutation(s): 0 
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSK4

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL32
f
130Leishmania donovaniMutation(s): 0 
Find proteins for E9BFJ5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFJ5

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL33
g
125Leishmania donovaniMutation(s): 0 
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BR22

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL34
h
125Leishmania donovaniMutation(s): 0 
Find proteins for E9BUA1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUA1

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL36
i
97Leishmania donovaniMutation(s): 0 
Find proteins for E9BF65 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BF65

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL37
j
80Leishmania donovaniMutation(s): 0 
Gene Names: RPL37
Find proteins for P62885 (Leishmania donovani)
Go to UniProtKB:  P62885

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL38
k
76Leishmania donovaniMutation(s): 0 
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B7P2

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL39
l
50Leishmania donovaniMutation(s): 0 
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BCX6

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL40
m
50Leishmania donovaniMutation(s): 0 
Find proteins for E9BMW6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMW6

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL41
n
33Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL43
o
90Leishmania donovaniMutation(s): 0 
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFK4

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL44
p
96Leishmania donovaniMutation(s): 0 
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BBL5

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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

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

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

Download CCD File 
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

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