6MUW

The structure of the Plasmodium falciparum 20S proteasome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The structure of the PA28-20S proteasome complex from Plasmodium falciparum and implications for proteostasis.

Xie, S.C.Metcalfe, R.D.Hanssen, E.Yang, T.Gillett, D.L.Leis, A.P.Morton, C.J.Kuiper, M.J.Parker, M.W.Spillman, N.J.Wong, W.Tsu, C.Dick, L.R.Griffin, M.D.W.Tilley, L.

(2019) Nat Microbiol 4: 1990-2000

  • DOI: https://doi.org/10.1038/s41564-019-0524-4
  • Primary Citation of Related Structures:  
    6DFK, 6MUV, 6MUW, 6MUX

  • PubMed Abstract: 

    The activity of the proteasome 20S catalytic core is regulated by protein complexes that bind to one or both ends. The PA28 regulator stimulates 20S proteasome peptidase activity in vitro, but its role in vivo remains unclear. Here, we show that genetic deletion of the PA28 regulator from Plasmodium falciparum (Pf) renders malaria parasites more sensitive to the antimalarial drug dihydroartemisinin, indicating that PA28 may play a role in protection against proteotoxic stress. The crystal structure of PfPA28 reveals a bell-shaped molecule with an inner pore that has a strong segregation of charges. Small-angle X-ray scattering shows that disordered loops, which are not resolved in the crystal structure, extend from the PfPA28 heptamer and surround the pore. Using single particle cryo-electron microscopy, we solved the structure of Pf20S in complex with one and two regulatory PfPA28 caps at resolutions of 3.9 and 3.8 Å, respectively. PfPA28 binds Pf20S asymmetrically, strongly engaging subunits on only one side of the core. PfPA28 undergoes rigid body motions relative to Pf20S. Molecular dynamics simulations support conformational flexibility and a leaky interface. We propose lateral transfer of short peptides through the dynamic interface as a mechanism facilitating the release of proteasome degradation products.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-1 subunitA,
V [auth O]
260Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-2 subunitB,
W [auth P]
235Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-3 subunitAA [auth Q],
C
246Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-4 subunitD,
S [auth R]
241Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-5 subunitE,
O [auth S]
256Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-6 subunit
F, T
254Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-7 subunitBA [auth U],
G
252Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-1 subunitH,
Z [auth V]
252Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-2 subunitI,
U [auth W]
229Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-3 subunitJ,
P [auth X]
218Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-4 subunitK,
Q [auth Y]
195Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-5 subunitL,
X [auth Z]
211Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-6 subunitM,
Y [auth a]
240Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-7 subunitN,
R [auth b]
265Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection, Data processing
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-15
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references, Refinement description