9PTQ | pdb_00009ptq

Structure of Acb2 homolog 43 in complex with 3'cADPR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: in silico
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Literature

Functional diversity of phage sponge proteins that sequester host immune signals.

Hadary, R.Chang, R.B.Bechon, N.Tal, N.Osterman, I.Yirmiya, E.Garb, J.Amitai, G.Kranzusch, P.J.Sorek, R.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.08.24.671296
  • Primary Citation of Related Structures:  
    9PTQ

  • PubMed Abstract: 

    Multiple bacterial immune systems, including CBASS, Thoeris, and Pycsar, employ signaling molecules that activate the immune response following phage infection. Phages counteract bacterial immune signaling using sponge proteins that bind and sequester the immune signals, but the breadth of immune signals targeted by phage sponges is unclear. Here we study the functional versatility of Acb2, Tad1 and Tad2, three families of sponge proteins known to inhibit CBASS and Thoeris signaling. Eighty-four proteins representing the phylogenetic diversity of these sponge families were tested for their ability to inhibit immunity by sequestering 3'3'-cGAMP and 3'3'-cUA (CBASS), cCMP and cUMP (Pycsar), and 3'cADPR, His-ADPR and N7-cADPR (types I, II and IV Thoeris, respectively). While Acb2 proteins were so far reported to inhibit only CBASS systems, we found Acb2 homologs that bind 3'cADPR and inhibit Thoeris defense. In addition, we discovered sponge proteins that inhibit Pycsar and type IV Thoeris by binding cUMP and N7-cADPR, respectively. Using crystal structures, structural modeling and biochemical analyses, we explain the molecular basis for signal-binding specificities in members of these sponge families. Our study reports the first sponges inhibiting Pycsar and type IV Thoeris, and demonstrates how phage sponges evolve to obtain diverse specificities.


  • Organizational Affiliation
    • Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acb2 homolog 43
A, B, C, D, E
A, B, C, D, E, F
76phage metagenomeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OJC (Subject of Investigation/LOI)
Query on OJC

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]
(2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione
C15 H21 N5 O13 P2
NDSLKXAJVDJCEG-ZQSHOCFMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.123α = 90
b = 53.668β = 110.489
c = 73.479γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
RAPDdata 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 States1DP2 GM146250-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release