8G6E

Structure of the Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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Literature

Structures revealing mechanisms of resistance and collateral sensitivity of Plasmodium falciparum to proteasome inhibitors.

Hsu, H.C.Li, D.Zhan, W.Ye, J.Liu, Y.J.Leung, A.Qin, J.Crespo, B.Gamo, F.J.Zhang, H.Cui, L.Roth, A.Kirkman, L.A.Li, H.Lin, G.

(2023) Nat Commun 14: 8302-8302

  • DOI: https://doi.org/10.1038/s41467-023-44077-2
  • Primary Citation of Related Structures:  
    8G6E, 8G6F, 8UD9

  • PubMed Abstract: 

    The proteasome of the malaria parasite Plasmodium falciparum (Pf20S) is an advantageous drug target because its inhibition kills P. falciparum in multiple stages of its life cycle and synergizes with artemisinins. We recently developed a macrocyclic peptide, TDI-8304, that is highly selective for Pf20S over human proteasomes and is potent in vitro and in vivo against P. falciparum. A mutation in the Pf20S β6 subunit, A117D, confers resistance to TDI-8304, yet enhances both enzyme inhibition and anti-parasite activity of a tripeptide vinyl sulfone β2 inhibitor, WLW-vs. Here we present the high-resolution cryo-EM structures of Pf20S with TDI-8304, of human constitutive proteasome with TDI-8304, and of Pf20Sβ6 A117D with WLW-vs that give insights into the species selectivity of TDI-8304, resistance to it, and the collateral sensitivity associated with resistance, including that TDI-8304 binds β2 and β5 in wild type Pf20S as well as WLW-vs binds β2 and β5 in Pf20Sβ6 A117D . We further show that TDI-8304 kills P. falciparum as quickly as chloroquine and artemisinin and is active against P. cynomolgi at the liver stage. This increases interest in using these structures to facilitate the development of Pf20S inhibitors that target multiple proteasome subunits and limit the emergence of resistance.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
A, O
260Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for W7JVP8 (Plasmodium falciparum (isolate NF54))
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UniProt GroupW7JVP8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
B, P
235Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for A0A2I0BQ13 (Plasmodium falciparum (isolate NF54))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
C, Q
246Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for W7KN95 (Plasmodium falciparum (isolate NF54))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
D, R
241Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for A0A2I0BS43 (Plasmodium falciparum (isolate NF54))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
E, S
256Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for A0A2I0BP34 (Plasmodium falciparum (isolate NF54))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
F, T
253Plasmodium falciparum NF54Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
G, U
252Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for W7K040 (Plasmodium falciparum (isolate NF54))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6
H, V
252Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for W7JUG8 (Plasmodium falciparum (isolate NF54))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
I, W
229Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for W7K1J4 (Plasmodium falciparum (isolate NF54))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
J, X
218Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for A0A2I0BXS0 (Plasmodium falciparum (isolate NF54))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
K, Y
195Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for W7JKG5 (Plasmodium falciparum (isolate NF54))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
L, Z
211Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for W7K6A8 (Plasmodium falciparum (isolate NF54))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth a],
M
240Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for A0A2I0BU46 (Plasmodium falciparum (isolate NF54))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth b],
N
265Plasmodium falciparum NF54Mutation(s): 0 
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX4788

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI143714

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-01-03
    Changes: Database references