6MUX

The structure of the Plasmodium falciparum 20S proteasome in complex with one PA28 activator


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-1 subunit
A, O
260Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IAR3 (Plasmodium falciparum (isolate 3D7))
Explore Q8IAR3 
Go to UniProtKB:  Q8IAR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IAR3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-2 subunit
B, P
235Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for C6KST3 (Plasmodium falciparum (isolate 3D7))
Explore C6KST3 
Go to UniProtKB:  C6KST3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6KST3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-3 subunit
C, Q
246Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IDG3 (Plasmodium falciparum (isolate 3D7))
Explore Q8IDG3 
Go to UniProtKB:  Q8IDG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IDG3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-4 subunit
D, R
241Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IDG2 (Plasmodium falciparum (isolate 3D7))
Explore Q8IDG2 
Go to UniProtKB:  Q8IDG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IDG2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-5 subunit
E, S
256Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IBI3 (Plasmodium falciparum (isolate 3D7))
Explore Q8IBI3 
Go to UniProtKB:  Q8IBI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IBI3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-6 subunit
F, T
254Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IK90 (Plasmodium falciparum (isolate 3D7))
Explore Q8IK90 
Go to UniProtKB:  Q8IK90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IK90
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome alpha-7 subunit
G, U
252Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for O77396 (Plasmodium falciparum (isolate 3D7))
Explore O77396 
Go to UniProtKB:  O77396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO77396
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-1 subunit
H, V
252Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8I0U7 (Plasmodium falciparum (isolate 3D7))
Explore Q8I0U7 
Go to UniProtKB:  Q8I0U7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I0U7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-2 subunit
I, W
229Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8I6T3 (Plasmodium falciparum (isolate 3D7))
Explore Q8I6T3 
Go to UniProtKB:  Q8I6T3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I6T3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-3 subunit
J, X
218Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8I261 (Plasmodium falciparum (isolate 3D7))
Explore Q8I261 
Go to UniProtKB:  Q8I261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I261
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-4 subunit
K, Y
195Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IKC9 (Plasmodium falciparum (isolate 3D7))
Explore Q8IKC9 
Go to UniProtKB:  Q8IKC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IKC9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-5 subunit
L, Z
211Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IJT1 (Plasmodium falciparum (isolate 3D7))
Explore Q8IJT1 
Go to UniProtKB:  Q8IJT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IJT1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-6 subunitAA [auth a],
M
240Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
20S proteasome beta-7 subunitBA [auth b],
N
265Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q7K6A9 (Plasmodium falciparum (isolate 3D7))
Explore Q7K6A9 
Go to UniProtKB:  Q7K6A9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7K6A9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome activator PA28279Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0907700
UniProt
Find proteins for Q8I374 (Plasmodium falciparum (isolate 3D7))
Explore Q8I374 
Go to UniProtKB:  Q8I374
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I374
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Refinement description