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), 0.222 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8R66

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 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.

Macromolecule Content 

  • Total Structure Weight: 59.48 kDa 
  • Atom Count: 3,614 
  • Modeled Residue Count: 418 
  • Deposited Residue Count: 506 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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), 0.222 (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