8V6Q | pdb_00008v6q

Crystal structure of EcThsA in ligand-free state

• PDB DOI: https://doi.org/10.2210/pdb8V6Q/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-02 Released: 2024-06-12 
• Deposition Author(s): Shi, Y., Masic, V., Mosaiab, T., Goulart, C.C., Hartley-Tassell, L., Sorbello, M., Vasquez, V., Mishra, B.P., Holt, S., Gu, W., Kobe, B., Ve, T.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.269 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of macro domain-containing Thoeris antiphage defense systems.

Shi, Y., Masic, V., Mosaiab, T., Rajaratman, P., Hartley-Tassell, L., Sorbello, M., Goulart, C.C., Vasquez, E., Mishra, B.P., Holt, S., Gu, W., Kobe, B., Ve, T.

(2024) Sci Adv 10: eadn3310-eadn3310

• PubMed: 38924412 
• DOI: https://doi.org/10.1126/sciadv.adn3310
• Primary Citation Related Structures: 
  8V6Q, 8V6R, 8V6S, 8V6T


• PubMed Abstract: 
  

  Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate signaling nucleotides that activate ThsA effectors. Silent information regulator and SMF/DprA-LOG (SIR2-SLOG) containing ThsA effectors are activated by cyclic ADP-ribose (ADPR) isomers 2'cADPR and 3'cADPR, triggering abortive infection via nicotinamide adenine dinucleotide (NAD ⁺ ) depletion. Here, we characterize Thoeris systems with transmembrane and macro domain (TM-macro)-containing ThsA effectors. We demonstrate that ThsA macro domains bind ADPR and imidazole adenine dinucleotide (IAD), but not 2'cADPR or 3'cADPR. Combining crystallography, in silico predictions, and site-directed mutagenesis, we show that ThsA macro domains form nucleotide-induced higher-order oligomers, enabling TM domain clustering. We demonstrate that ThsB can produce both ADPR and IAD, and we identify a ThsA TM-macro-specific ThsB subfamily with an active site resembling deoxy-nucleotide and deoxy-nucleoside processing enzymes. Collectively, our study demonstrates that Thoeris systems with SIR2-SLOG and TM-macro ThsA effectors trigger abortive infection via distinct mechanisms.

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Organizational Affiliation: 
• Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia.
Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.61 kDa 
• Atom Count: 3,446 
• Modeled Residue Count: 421 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thoeris protein ThsA Macro domain-containing protein	A, B	241	Escherichia coli	Mutation(s): 0  Gene Names: FPI65_12015
UniProt
Find proteins for A0A178STJ6 (Escherichia coli) Explore A0A178STJ6  Go to UniProtKB:  A0A178STJ6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.269 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.036	α = 90
b = 93.541	β = 90
c = 140.541	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Shi, Y., Masic, V., Mosaiab, T., Goulart, C.C., Hartley-Tassell, L., Sorbello, M., Vasquez, V., Mishra, B.P., Holt, S., Gu, W., Kobe, B., Ve, T.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FT200100572

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 1.1: 2024-07-10
  Changes: Database references