5OUQ | pdb_00005ouq

Structure of TgPLP1 MACPF domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.11 Å
  • R-Value Free: 
    0.298 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.287 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 
    0.287 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Structures of monomeric and oligomeric forms of theToxoplasma gondiiperforin-like protein 1.

Ni, T.Williams, S.I.Rezelj, S.Anderluh, G.Harlos, K.Stansfeld, P.J.Gilbert, R.J.C.

(2018) Sci Adv 4: eaaq0762-eaaq0762

  • DOI: https://doi.org/10.1126/sciadv.aaq0762
  • Primary Citation Related Structures: 
    5OUO, 5OUP, 5OUQ, 5OWN

  • PubMed Abstract: 

    Toxoplasma and Plasmodium are the parasitic agents of toxoplasmosis and malaria, respectively, and use perforin-like proteins (PLPs) to invade host organisms and complete their life cycles. The Toxoplasma gondii PLP1 ( Tg PLP1) is required for efficient exit from parasitophorous vacuoles in which proliferation occurs. We report structures of the membrane attack complex/perforin (MACPF) and Apicomplexan PLP C-terminal β-pleated sheet (APCβ) domains of Tg PLP1. The MACPF domain forms hexameric assemblies, with ring and helix geometries, and the APCβ domain has a novel β-prism fold joined to the MACPF domain by a short linker. Molecular dynamics simulations suggest that the helical MACPF oligomer preserves a biologically important interface, whereas the APCβ domain binds preferentially through a hydrophobic loop to membrane phosphatidylethanolamine, enhanced by the additional presence of inositol phosphate lipids. This mode of membrane binding is supported by site-directed mutagenesis data from a liposome-based assay. Together, these structural and biophysical findings provide insights into the molecular mechanism of membrane targeting by Tg PLP1.


  • Organizational Affiliation
    • Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecule Content 

  • Total Structure Weight: 236 kDa 
  • Atom Count: 12,948 
  • Modeled Residue Count: 1,656 
  • Deposited Residue Count: 2,136 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Perforin-like protein 1356Toxoplasma gondiiMutation(s): 0 
Gene Names: PLP1
UniProt
Find proteins for V5BCL0 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore V5BCL0 
Go to UniProtKB:  V5BCL0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5BCL0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.11 Å
  • R-Value Free:  0.298 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.287 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 0.287 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.49α = 90
b = 185.74β = 121.48
c = 104.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N000331/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-11-13
    Changes: Structure summary