8ZVC | pdb_00008zvc

ShosT with PRPP-Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

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

Validation slider image for 8ZVC

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

A toxin-antitoxin system provides phage defense via DNA damage and repair.

Pu, H.Chen, Y.Zhao, X.Dai, L.Tong, A.Tang, D.Chen, Q.Yu, Y.

(2025) Nat Commun 16: 3141-3141

  • DOI: https://doi.org/10.1038/s41467-025-58540-9
  • Primary Citation Related Structures: 
    8ZVA, 8ZVB, 8ZVC, 8ZVD

  • PubMed Abstract: 

    Widespread in bacteria and archaea, toxin-antitoxin (TA) systems have been recently demonstrated to function in phage defense. Here we characterize the anti-phage function of a type IV TA system, ShosTA. Using structural and biochemical approaches, we show that ShosT couples phosphoribosyltransferase and pyrophosphatase activities to disrupt purine metabolism, resulting in DNA duplication, cell filamentation and ultimate cell death. ShosA binds DNA and likely recruits other proteins to facilitate DNA homologous recombination to antagonize ShosT's toxicity. We identify Gp0.7 of T7 phage as a trigger for ShosTA system via shutting off the protein synthesis, and the C-terminus-mediated intrinsic instability of ShosA releases the toxicity of the existing ShosT proteins. Collectively, our results provide a novel toxin-antitoxin mechanism for anti-phage immunity and shed light on the triggering of this TA system.


  • Organizational Affiliation
    • Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.

Macromolecule Content 

  • Total Structure Weight: 50.08 kDa 
  • Atom Count: 3,950 
  • Modeled Residue Count: 424 
  • Deposited Residue Count: 432 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ShosT432Escherichia coli APEC O1Mutation(s): 0 
Gene Names: APECO1_1183
UniProt
Find proteins for A0A0H2Z117 (Escherichia coli O1:K1 / APEC)
Explore A0A0H2Z117 
Go to UniProtKB:  A0A0H2Z117
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2Z117
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRP
(Subject of Investigation/LOI)

Query on PRP



Download:Ideal Coordinates CCD File
B [auth A]1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
MES
(Subject of Investigation/LOI)

Query on MES



Download:Ideal Coordinates CCD File
C [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
(Subject of Investigation/LOI)

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.779α = 90
b = 79.153β = 90
c = 89.988γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references