5NNW

NLPPya in complex with glucosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins.

Lenarcic, T.Albert, I.Bohm, H.Hodnik, V.Pirc, K.Zavec, A.B.Podobnik, M.Pahovnik, D.Zagar, E.Pruitt, R.Greimel, P.Yamaji-Hasegawa, A.Kobayashi, T.Zienkiewicz, A.Gomann, J.Mortimer, J.C.Fang, L.Mamode-Cassim, A.Deleu, M.Lins, L.Oecking, C.Feussner, I.Mongrand, S.Anderluh, G.Nurnberger, T.

(2017) Science 358: 1431-1434

  • DOI: https://doi.org/10.1126/science.aan6874
  • Primary Citation of Related Structures:  
    5NNW, 5NO9

  • PubMed Abstract: 

    Necrosis and ethylene-inducing peptide 1-like (NLP) proteins constitute a superfamily of proteins produced by plant pathogenic bacteria, fungi, and oomycetes. Many NLPs are cytotoxins that facilitate microbial infection of eudicot, but not of monocot plants. Here, we report glycosylinositol phosphorylceramide (GIPC) sphingolipids as NLP toxin receptors. Plant mutants with altered GIPC composition were more resistant to NLP toxins. Binding studies and x-ray crystallography showed that NLPs form complexes with terminal monomeric hexose moieties of GIPCs that result in conformational changes within the toxin. Insensitivity to NLP cytolysins of monocot plants may be explained by the length of the GIPC head group and the architecture of the NLP sugar-binding site. We unveil early steps in NLP cytolysin action that determine plant clade-specific toxin selectivity.


  • Organizational Affiliation

    Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
25 kDa protein elicitor
A, B, C, D
219Pythium aphanidermatumMutation(s): 0 
Gene Names: SD21-1
UniProt
Find proteins for Q9SPD4 (Pythium aphanidermatum)
Explore Q9SPD4 
Go to UniProtKB:  Q9SPD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SPD4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.996α = 90
b = 122.285β = 90
c = 121.099γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaJ1-7515
Slovenian Research AgencySloveniaP1-0391

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary