8V3E | pdb_00008v3e

Structure of Myroides odoratus phage Tad2 in apo state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.273 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 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
Tad2A [auth E],
B [auth F],
C [auth A],
D [auth B]
88Myroides odoratusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.273 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.206α = 90
b = 93.206β = 90
c = 235.549γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The G. Harold and Leila Y. Mathers FoundationUnited States--
The Pew Charitable TrustsUnited States--

Revision History  (Full details and data files)

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