6O0W

Crystal structure of the TIR domain from the grapevine disease resistance protein RUN1 in complex with NADP+ and Bis-Tris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

NAD+cleavage activity by animal and plant TIR domains in cell death pathways.

Horsefield, S.Burdett, H.Zhang, X.Manik, M.K.Shi, Y.Chen, J.Qi, T.Gilley, J.Lai, J.S.Rank, M.X.Casey, L.W.Gu, W.Ericsson, D.J.Foley, G.Hughes, R.O.Bosanac, T.von Itzstein, M.Rathjen, J.P.Nanson, J.D.Boden, M.Dry, I.B.Williams, S.J.Staskawicz, B.J.Coleman, M.P.Ve, T.Dodds, P.N.Kobe, B.

(2019) Science 365: 793-799

  • DOI: 10.1126/science.aax1911
  • Primary Citation of Related Structures:  
    6O0R, 6O0Q, 6O0T, 6O0S, 6O0V, 6O0U, 6O1B, 6O0W

  • PubMed Abstract: 
  • SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of nicotinamide adenine dinucleotide in its oxidized form (NAD + ) during Wallerian degeneration associated with neuropathies. Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effector proteins and trigger localized cell death to restrict pathogen infection ...

    SARM1 (sterile alpha and TIR motif containing 1) is responsible for depletion of nicotinamide adenine dinucleotide in its oxidized form (NAD + ) during Wallerian degeneration associated with neuropathies. Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors recognize pathogen effector proteins and trigger localized cell death to restrict pathogen infection. Both processes depend on closely related Toll/interleukin-1 receptor (TIR) domains in these proteins, which, as we show, feature self-association-dependent NAD + cleavage activity associated with cell death signaling. We further show that SARM1 SAM (sterile alpha motif) domains form an octamer essential for axon degeneration that contributes to TIR domain enzymatic activity. The crystal structures of ribose and NADP + (the oxidized form of nicotinamide adenine dinucleotide phosphate) complexes of SARM1 and plant NLR RUN1 TIR domains, respectively, reveal a conserved substrate binding site. NAD + cleavage by TIR domains is therefore a conserved feature of animal and plant cell death signaling pathways.


    Organizational Affiliation

    School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia. b.kobe@uq.edu.au t.ve@griffith.edu.au peter.dodds@csiro.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TIR-NB-LRR type resistance protein RUN1A179Vitis rotundifoliaMutation(s): 0 
Gene Names: RUN1
EC: 3.2.2.6 (UniProt), 3.2.2 (UniProt)
UniProt
Find proteins for V9M398 (Vitis rotundifolia)
Explore V9M398 
Go to UniProtKB:  V9M398
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2P
Query on A2P

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-2'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
AEOBEOJCBAYXBA-KQYNXXCUSA-N
 Ligand Interaction
BTB
Query on BTB

Download Ideal Coordinates CCD File 
C [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.085α = 90
b = 79.399β = 107.42
c = 34.266γ = 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
National Health and Medical Research Council (NHMRC, Australia)Australia1107804
National Health and Medical Research Council (NHMRC, Australia)Australia1160570
National Health and Medical Research Council (NHMRC, Australia)Australia1071659
National Health and Medical Research Council (NHMRC, Australia)Australia1108859
Australian Research Council (ARC)AustraliaDP160102244
Australian Research Council (ARC)AustraliaDP190102526

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence