X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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The structure of "defective in induced resistance" protein of Arabidopsis thaliana, DIR1, reveals a new type of lipid transfer protein.

Lascombe, M.B.Bakan, B.Buhot, N.Marion, D.Blein, J.P.Larue, V.Lamb, C.Prange, T.

(2008) Protein Sci 17: 1522-1530

  • DOI: https://doi.org/10.1110/ps.035972.108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Screening of transfer DNA (tDNA) tagged lines of Arabidopsis thaliana for mutants defective in systemic acquired resistance led to the characterization of dir1-1 (defective in induced resistance [systemic acquired resistance, SAR]) mutant. It has been suggested that the protein encoded by the dir1 gene, i.e., DIR1, is involved in the long distance signaling associated with SAR. DIR1 displays the cysteine signature of lipid transfer proteins, suggesting that the systemic signal could be lipid molecules. However, previous studies have shown that this signature is not sufficient to define a lipid transfer protein, i.e., a protein capable of binding lipids. In this context, the lipid binding properties and the structure of a DIR1-lipid complex were both determined by fluorescence and X-ray diffraction. DIR1 is able to bind with high affinity two monoacylated phospholipids (dissociation constant in the nanomolar range), mainly lysophosphatidyl cholines, side-by-side in a large internal tunnel. Although DIR1 shares some structural and lipid binding properties with plant LTP2, it displays some specific features that define DIR1 as a new type of plant lipid transfer protein. The signaling function associated with DIR1 may be related to a specific lipid transport that needs to be characterized and to an additional mechanism of recognition by a putative receptor, as the structure displays on the surface the characteristic PxxP structural motif reminiscent of SH3 domain signaling pathways.

  • Organizational Affiliation

    Université Paris Descartes, CNRS, Laboratoire de Cristallographie et RMN Biologiques (UMR 8015), Paris 75006, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIR1 protein77Arabidopsis thalianaMutation(s): 0 
Gene Names: DIR1
Find proteins for Q8W453 (Arabidopsis thaliana)
Explore Q8W453 
Go to UniProtKB:  Q8W453
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8W453
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LP3 Binding MOAD:  2RKN Kd: 60 (nM) from 1 assay(s)
PDBBind:  2RKN Kd: 60 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.655α = 90
b = 48.217β = 90
c = 54.406γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MxCuBEdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance