6O0Q

Crystal structure of the TIR domain from human SARM1 in complex with ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 2.0 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
Sterile alpha and TIR motif-containing protein 1A, B144Homo sapiensMutation(s): 0 
Gene Names: SARM1KIAA0524SAMD2SARM
EC: 3.2.2.6 (UniProt), 3.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6SZW1 (Homo sapiens)
Explore Q6SZW1 
Go to UniProtKB:  Q6SZW1
PHAROS:  Q6SZW1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BDR (Subject of Investigation/LOI)
Query on BDR

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]beta-D-ribofuranose
C5 H10 O5
HMFHBZSHGGEWLO-TXICZTDVSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.986α = 90
b = 86.019β = 90
c = 116.684γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



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, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary