8R66 | pdb_00008r66

Crystal structure of ThsA Macro domain in complex with signaling molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.226 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

TIR domains produce histidine-ADPR as an immune signal in bacteria.

Sabonis, D.Avraham, C.Chang, R.B.Lu, A.Herbst, E.Silanskas, A.Vilutis, D.Leavitt, A.Yirmiya, E.Toyoda, H.C.Ruksenaite, A.Zaremba, M.Osterman, I.Amitai, G.Kranzusch, P.J.Sorek, R.Tamulaitiene, G.

(2025) Nature 642: 467-473

  • DOI: https://doi.org/10.1038/s41586-025-08930-2
  • Primary Citation of Related Structures:  
    8R66, 8V3E, 9EIB

  • PubMed Abstract: 

    Toll/interleukin-1 receptor (TIR) domains are central components of pattern recognition immune proteins across all domains of life 1,2 . In bacteria and plants, TIR-domain proteins recognize pathogen invasion and then produce immune signalling molecules exclusively comprising nucleotide moieties 2-5 . Here we show that the TIR-domain protein of the type II Thoeris defence system in bacteria produces a unique signalling molecule comprising the amino acid histidine conjugated to ADP-ribose (His-ADPR). His-ADPR is generated in response to phage infection and activates the cognate Thoeris effector by binding a Macro domain located at the C terminus of the effector protein. By determining the crystal structure of a ligand-bound Macro domain, we describe the structural basis for His-ADPR and its recognition and show its role by biochemical and mutational analyses. Our analyses furthermore reveal a family of phage proteins that bind and sequester His-ADPR signalling molecules, enabling phages to evade TIR-mediated immunity. These data demonstrate diversity in bacterial TIR signalling and reveal a new class of TIR-derived immune signalling molecules that combine nucleotide and amino acid moieties.


  • Organizational Affiliation
    • Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thoeris protein ThsA
A, B
253Bacillus amyloliquefaciensMutation(s): 0 
Gene Names: thsA
UniProt
Find proteins for I2C645 (Bacillus amyloliquefaciens (strain Y2))
Explore I2C645 
Go to UniProtKB:  I2C645
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI2C645
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y65 (Subject of Investigation/LOI)
Query on Y65

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
(2~{S})-3-[1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]imidazol-4-yl]-2-azanyl-propanoic acid
C21 H30 N8 O15 P2
NPNIPERJQFLOGA-KQRTYHPUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.296α = 90
b = 71.059β = 96.78
c = 51.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of LithuaniaLithuaniaS-MIP-21-6

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references
  • Version 1.2: 2025-05-14
    Changes: Database references
  • Version 1.3: 2025-06-25
    Changes: Database references