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 5L7S | pdb_00005l7s

Crystal structure of RXLR effector PexRD54 from Phytophthora infestans

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.256 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5L7S

This is version 1.3 of the entry. See complete history. 

Literature

Structural Basis of Host Autophagy-related Protein 8 (ATG8) Binding by the Irish Potato Famine Pathogen Effector Protein PexRD54.

Maqbool, A., Hughes, R.K., Dagdas, Y.F., Tregidgo, N., Zess, E., Belhaj, K., Round, A., Bozkurt, T.O., Kamoun, S., Banfield, M.J.

(2016) J Biol Chem 291: 20270-20282

  • DOI: https://doi.org/10.1074/jbc.M116.744995
  • Primary Citation Related Structures: 
    5L7S, 5L83

  • PubMed Abstract: 

    Filamentous plant pathogens deliver effector proteins to host cells to promote infection. The Phytophthora infestans RXLR-type effector PexRD54 binds potato ATG8 via its ATG8 family-interacting motif (AIM) and perturbs host-selective autophagy. However, the structural basis of this interaction remains unknown. Here, we define the crystal structure of PexRD54, which includes a modular architecture, including five tandem repeat domains, with the AIM sequence presented at the disordered C terminus. To determine the interface between PexRD54 and ATG8, we solved the crystal structure of potato ATG8CL in complex with a peptide comprising the effector's AIM sequence, and we established a model of the full-length PexRD54-ATG8CL complex using small angle x-ray scattering. Structure-informed deletion of the PexRD54 tandem domains reveals retention of ATG8CL binding in vitro and in planta This study offers new insights into structure/function relationships of oomycete RXLR effectors and how these proteins engage with host cell targets to promote disease.

    • Organizational Affiliation: 
    • From the Department of Biological Chemistry, John Innes Centre, and.

Macromolecule Content 

  • Total Structure Weight: 34.07 kDa 
  • Atom Count: 2,224 
  • Modeled Residue Count: 267 
  • Deposited Residue Count: 292 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Secreted RxLR effector peptide protein292Phytophthora infestansMutation(s): 0 
Gene Names: PITG_09316
UniProt
Find proteins for D0NBE6 (Phytophthora infestans (strain T30-4))
Explore D0NBE6 
Go to UniProtKB:  D0NBE6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0NBE6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.256 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.16α = 90
b = 89.16β = 90
c = 144.32γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomNGRB

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Structure summary
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Author supporting evidence, Data collection, Database references