6MUX

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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
20S proteasome alpha-1 subunit
A, O
260Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IAR3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IAR3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
20S proteasome alpha-2 subunit
B, P
235Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for C6KST3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C6KST3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
20S proteasome alpha-3 subunit
C, Q
246Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IDG3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IDG3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
20S proteasome alpha-4 subunit
D, R
241Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IDG2 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IDG2
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
20S proteasome alpha-5 subunit
E, S
256Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IBI3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IBI3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
20S proteasome alpha-6 subunit
F, T
254Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IK90 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IK90
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
20S proteasome alpha-7 subunit
G, U
252Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for O77396 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  O77396
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
20S proteasome beta-1 subunit
H, V
252Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8I0U7 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I0U7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
20S proteasome beta-2 subunit
I, W
229Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8I6T3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I6T3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
20S proteasome beta-3 subunit
J, X
218Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8I261 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I261
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
20S proteasome beta-4 subunit
K, Y
195Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IKC9 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IKC9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
20S proteasome beta-5 subunit
L, Z
211Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IJT1 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IJT1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
20S proteasome beta-6 subunit
M, a
240Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for C0H4E8 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C0H4E8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
20S proteasome beta-7 subunit
N, b
265Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q7K6A9 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q7K6A9
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Proteasome activator PA28
c, d, e, f, g, h, i
279Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
Find proteins for Q8I374 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I374
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

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--

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