5KU7

Crystal structure of the TIR domain from the Muscadinia rotundifolia disease resistance protein RPV1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.185 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure and Function of the TIR Domain from the Grape NLR Protein RPV1.

Williams, S.J.Yin, L.Foley, G.Casey, L.W.Outram, M.A.Ericsson, D.J.Lu, J.Boden, M.Dry, I.B.Kobe, B.

(2016) Front Plant Sci 7: 1850-1850

  • DOI: https://doi.org/10.3389/fpls.2016.01850
  • Primary Citation of Related Structures:  
    5KU7

  • PubMed Abstract: 

    The N-terminal Toll/interleukin-1 receptor/resistance protein (TIR) domain has been shown to be both necessary and sufficient for defense signaling in the model plants flax and Arabidopsis . In examples from these organisms, TIR domain self-association is required for signaling function, albeit through distinct interfaces. Here, we investigate these properties in the TIR domain containing resistance protein RPV1 from the wild grapevine Muscadinia rotundifolia . The RPV1 TIR domain, without additional flanking sequence present, is autoactive when transiently expressed in tobacco, demonstrating that the TIR domain alone is capable of cell-death signaling. We determined the crystal structure of the RPV1 TIR domain at 2.3 Å resolution. In the crystals, the RPV1 TIR domain forms a dimer, mediated predominantly through residues in the αA and αE helices ("AE" interface). This interface is shared with the interface discovered in the dimeric complex of the TIR domains from the Arabidopsis RPS4/RRS1 resistance protein pair. We show that surface-exposed residues in the AE interface that mediate the dimer interaction in the crystals are highly conserved among plant TIR domain-containing proteins. While we were unable to demonstrate self-association of the RPV1 TIR domain in solution or using yeast 2-hybrid, mutations of surface-exposed residues in the AE interface prevent the cell-death autoactive phenotype. In addition, mutation of residues known to be important in the cell-death signaling function of the flax L6 TIR domain were also shown to be required for RPV1 TIR domain mediated cell-death. Our data demonstrate that multiple TIR domain surfaces control the cell-death function of the RPV1 TIR domain and we suggest that the conserved AE interface may have a general function in TIR-NLR signaling.


  • Organizational Affiliation

    School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, BrisbaneQLD, Australia; Research School of Biology, The Australian National University, CanberraACT, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TIR-NB-LRR type resistance protein RPV1
A, B
177Vitis rotundifoliaMutation(s): 0 
Gene Names: RPV1
EC: 3.2.2.6
UniProt
Find proteins for V9M2S5 (Vitis rotundifolia)
Explore V9M2S5 
Go to UniProtKB:  V9M2S5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV9M2S5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.185 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.855α = 90
b = 89.117β = 90
c = 113.858γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP120100685
Australian Research Council (ARC)AustraliaDP160102244

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary