6DFK

Crystal structure of the 11S subunit of the Plasmodium falciparum proteasome, PA28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/s41564-019-0524-4
  • Primary Citation of Related Structures:  

  • 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 gene ...

    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

    Oncology Clinical R&D, Takeda Pharmaceuticals International Co., Cambridge, MA, USA.,Australian Cancer Research Foundation Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Infection and Immunity Division, The Walter and Eliza Hall Institute, Parkville, Victoria, Australia.,Data61 CSIRO, Docklands, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.,Advanced Microscopy Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia. ltilley@unimelb.edu.au.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia. mgriffin@unimelb.edu.au.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Subunit of proteaseome activator complex,putative
A, B, C, D, E, F, G, H, I, J, K, L, M, N
280Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
Find proteins for Q8I374 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I374
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 166.485α = 90.00
b = 166.485β = 90.00
c = 399.162γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)Australia--
Australian Research CouncilAustralia--
Global Health Innovative Technology Fund--
GSK Tres Cantos Open Lab Foundation--

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Type: Data collection, Database references
  • Version 1.2: 2019-11-06
    Type: Data collection, Database references