6MUV

The structure of the Plasmodium falciparum 20S proteasome in complex with two PA28 activators


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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:  
    6MUW, 6MUV, 6MUX, 6DFK

  • 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

    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia. ltilley@unimelb.edu.au.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome alpha-1 subunitAO260Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0807500
EC: 3.4.25.1
Find proteins for Q8IAR3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome alpha-2 subunitBP235Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0608500
EC: 3.4.25.1
Find proteins for C6KST3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome alpha-4 subunitDR241Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1353900
EC: 3.4.25.1
Find proteins for Q8IDG2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome alpha-5 subunitES256Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0727400
EC: 3.4.25.1
Find proteins for Q8IBI3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome alpha-6 subunitFT254Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1474800
EC: 3.4.25.1
Find proteins for Q8IK90 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome alpha-7 subunitGU252Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0317000
EC: 3.4.25.1
Find proteins for O77396 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome beta-1 subunitHV252Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0931800
EC: 3.4.25.1
Find proteins for Q8I0U7 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome beta-3 subunitJX218Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0108000
EC: 3.4.25.1
Find proteins for Q8I261 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome beta-4 subunitKY195Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1470900
EC: 3.4.25.1
Find proteins for Q8IKC9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome beta-6 subunitMa240Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome beta-7 subunitNb265Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0803800
EC: 3.4.25.1
Find proteins for Q7K6A9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome activator PA28cdefghijklmnop279Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0907700
Find proteins for Q8I374 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome beta-5 subunitLZ211Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1011400
EC: 3.4.25.1
Find proteins for Q8IJT1 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome alpha-3 subunitCQ246Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1353800
EC: 3.4.25.1
Find proteins for Q8IDG3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
20S proteasome beta-2 subunitIW229Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1328100
EC: 3.4.25.1
Find proteins for Q8I6T3 (Plasmodium falciparum (isolate 3D7))
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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 

  • 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