9EIB | pdb_00009eib

Structure of Myroides odoratus prophage anti-Thoeris 2 (ModTad2) in complex with hisADPR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 
    0.237 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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: 20.68 kDa 
  • Atom Count: 1,637 
  • Modeled Residue Count: 173 
  • Deposited Residue Count: 178 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prophage anti-Thoeris 2 (ModTad2)
A, B
89Myroides odoratusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y65
(Subject of Investigation/LOI)

Query on Y65



Download:Ideal Coordinates CCD File
C [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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.237 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.692α = 90
b = 92.692β = 90
c = 78.079γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1DP2GM146250-01

Revision History  (Full details and data files)

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