6DFK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    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 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. ltilley@unimelb.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Subunit of proteaseome activator complex,putative
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N
280Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0907700
UniProt
Find proteins for Q8I374 (Plasmodium falciparum (isolate 3D7))
Explore Q8I374 
Go to UniProtKB:  Q8I374
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , AB [auth J] , BA [auth D] , BB [auth J] , CA [auth D] , CB [auth J] , DA [auth D] , DB [auth J] , 
AA [auth C], AB [auth J], BA [auth D], BB [auth J], CA [auth D], CB [auth J], DA [auth D], DB [auth J], EA [auth D], EB [auth J], FA [auth E], FB [auth K], GA [auth E], GB [auth K], HA [auth E], HB [auth K], IA [auth E], IB [auth K], JA [auth F], JB [auth L], KA [auth F], KB [auth L], LA [auth F], LB [auth L], MA [auth F], MB [auth L], NA [auth F], NB [auth M], O [auth A], OA [auth G], OB [auth M], P [auth A], PA [auth G], PB [auth M], Q [auth A], QA [auth G], QB [auth M], R [auth A], RA [auth G], RB [auth M], S [auth B], SA [auth H], SB [auth N], T [auth B], TA [auth H], TB [auth N], U [auth B], UA [auth H], UB [auth N], V [auth B], VA [auth I], VB [auth N], W [auth B], WA [auth I], X [auth C], XA [auth I], Y [auth C], YA [auth I], Z [auth C], ZA [auth I]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.485α = 90
b = 166.485β = 90
c = 399.162γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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--
Global Health Innovative Technology Fund--
GSK Tres Cantos Open Lab Foundation--

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: 2020-01-01
    Changes: Author supporting evidence