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 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

Validation slider image for 8V3E

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 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: 39.62 kDa 
  • Atom Count: 2,736 
  • Modeled Residue Count: 319 
  • Deposited Residue Count: 352 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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