7UXU

CryoEM structure of the TIR domain from AbTir in complex with 3AD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling.

Manik, M.K.Shi, Y.Li, S.Zaydman, M.A.Damaraju, N.Eastman, S.Smith, T.G.Gu, W.Masic, V.Mosaiab, T.Weagley, J.S.Hancock, S.J.Vasquez, E.Hartley-Tassell, L.Kargios, N.Maruta, N.Lim, B.Y.J.Burdett, H.Landsberg, M.J.Schembri, M.A.Prokes, I.Song, L.Grant, M.DiAntonio, A.Nanson, J.D.Guo, M.Milbrandt, J.Ve, T.Kobe, B.

(2022) Science 377: eadc8969-eadc8969

  • DOI: https://doi.org/10.1126/science.adc8969
  • Primary Citation of Related Structures:  
    7UWG, 7UXR, 7UXS, 7UXT, 7UXU

  • PubMed Abstract: 

    Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD + ) hydrolysis. We show that v-cADPR (2'cADPR) and v2-cADPR (3'cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2'cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3'cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and a suppressor of plant immunity when produced by the effector HopAM1. Collectively, our results reveal the molecular basis of cADPR isomer production and establish 3'cADPR in bacteria as an antiviral and plant immunity-suppressing signaling molecule.


  • Organizational Affiliation

    School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Molecular chaperone Tir
A, B, C, D
137Acinetobacter baumanniiMutation(s): 0 
Gene Names: APD31_10100H0529_09530
UniProt
Find proteins for A0A009IHW8 (Acinetobacter baumannii (strain 1295743))
Explore A0A009IHW8 
Go to UniProtKB:  A0A009IHW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A009IHW8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1O4 (Subject of Investigation/LOI)
Query on 1O4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(8-azanylisoquinolin-2-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C24 H30 N7 O13 P2
ZWKGBLKVIKZVCF-PAXFUWABSA-O
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references
  • Version 1.2: 2022-10-12
    Changes: Database references