9F9P | pdb_00009f9p

CryoEM structure of recombinant Trypanosoma cruzi apo proteasome 20S subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.25 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

Pharmacological and structural understanding of the Trypanosoma cruzi proteasome provides key insights for developing site-specific inhibitors.

Eadsforth, T.C.Torrie, L.S.Rowland, P.Edgar, E.V.MacLean, L.M.Paterson, C.Robinson, D.A.Shepherd, S.M.Thomas, J.Thomas, M.G.Gray, D.W.Postis, V.L.G.De Rycker, M.

(2024) J Biological Chem 301: 108049-108049

  • DOI: https://doi.org/10.1016/j.jbc.2024.108049
  • Primary Citation of Related Structures:  
    9F9P, 9F9T

  • PubMed Abstract: 

    The proteasome is considered an excellent drug target for many infectious diseases as well as cancer. Challenges with robust and safe supply of proteasomes from infectious agents, lack of structural information and complex pharmacology due to multiple active sites have hampered progress in the infectious disease space. We recombinantly expressed the proteasome of the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease, and demonstrate pharmacological equivalence to the native T. cruzi proteasome. Active-site mutant recombinant proteasomes reveal substrate promiscuity for wild-type proteasomes, with important implications for assessing pharmacological responses of active-site selective inhibitors. Using these mutant proteasomes, we show that some selective parasite proteasome inhibitors only partially inhibit the chymotrypsin-like activity, including a newly developed 5-(phenoxymethyl)furan-2-carboxamide-based proteasome inhibitor. In spite of partial inhibition, these compounds remain potent inhibitors of intracellular T. cruzi growth. Drug-resistant mutants provide further insights in drug mode-of-inhibition. We also present the high-resolution CryoEM structures of both native and recombinantly-expressed T. cruzi proteasomes which reveal pharmacologically-relevant differences in the ligand-binding site compared to the related Leishmania proteasome. Furthermore, we show that the trypanosomatid β4/β5 selectivity pocket is not present in the proteasome structures of other protozoan parasites. This work highlights the need, and provides approaches, to precisely assess proteasome substrate selectivity and pharmacology. It enables structure-guided drug discovery for this promising Chagas disease drug target, provides a new chemical starting point for drug discovery, and paves the road for development of robust proteasome drug discovery programmes for other eukaryotic infectious diseases.


  • Organizational Affiliation
    • Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK, DD1 5EH.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
A, O
268Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_2g302
UniProt
Find proteins for A0A2V2W7U6 (Trypanosoma cruzi)
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UniProt GroupA0A2V2W7U6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
B, P
231Trypanosoma cruziMutation(s): 0 
Gene Names: C3747_243g34C4B63_43g135
UniProt
Find proteins for A0A7J6YDC7 (Trypanosoma cruzi)
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UniProt GroupA0A7J6YDC7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
C, Q
286Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_25g312
UniProt
Find proteins for A0A2V2VJR6 (Trypanosoma cruzi)
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UniProt GroupA0A2V2VJR6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
D, R
247Trypanosoma cruziMutation(s): 0 
Gene Names: C3747_43g63C3747_44g28ECC02_002871
UniProt
Find proteins for V5BW71 (Trypanosoma cruzi Dm28c)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
E, S
245Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_43g129
UniProt
Find proteins for V5B1X4 (Trypanosoma cruzi Dm28c)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
F, T
265Trypanosoma cruziMutation(s): 0 
Gene Names: pr29AC4B63_48g135
UniProt
Find proteins for A0A7J6YFR6 (Trypanosoma cruzi)
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UniProt GroupA0A7J6YFR6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Putative proteasome alpha 7 subunit
G, U
237Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_12g396
UniProt
Find proteins for V5AWB3 (Trypanosoma cruzi Dm28c)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
H, V
284Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_89g44
UniProt
Find proteins for V5BHX1 (Trypanosoma cruzi Dm28c)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
I, W
292Trypanosoma cruziMutation(s): 0 
Gene Names: TCDM_00108
UniProt
Find proteins for V5BCU3 (Trypanosoma cruzi Dm28c)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Putative proteasome beta 3 subunit
J, X
205Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_112g19
UniProt
Find proteins for V5BGL9 (Trypanosoma cruzi Dm28c)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
K, Y
206Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_13g138
UniProt
Find proteins for V5C017 (Trypanosoma cruzi Dm28c)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta
L, Z
311Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_48g131
UniProt
Find proteins for V5BU39 (Trypanosoma cruzi Dm28c)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth a],
M
246Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_6g586
UniProt
Find proteins for A0A2V2VW62 (Trypanosoma cruzi)
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UniProt GroupA0A2V2VW62
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth b],
N
218Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_7g423
UniProt
Find proteins for A0A2V2VV98 (Trypanosoma cruzi)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0405

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-12-25 
  • Deposition Author(s): Rowland, P.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-08
    Changes: Data collection, Database references