9PD0 | pdb_00009pd0

Panoptes OptS minimal CRISPR polymerase (mCpol) with non-hydrolyzable ligand ApCpp from Klebsiella pneumoniae strain KP67

• PDB DOI: https://doi.org/10.2210/pdb9PD0/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-29 Released: 2025-09-24 
• Deposition Author(s): Dinh, D.M., Morehouse, B.R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.270 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: in silico

Literature

The Panoptes system uses decoy cyclic nucleotides to defend against phage.

Sullivan, A.E., Nabhani, A., Izrailevsky, D.S., Schinkel, K., Hoffman, C.R.K., Robbins, L.K., Nagy, T.A., Duncan, M.L., Ledvina, H.E., Erbse, A.H., Kibby, E.M., Tak, U., Dinh, D.M., Ednacot, E.M.Q., Nguyen, C.M., Burroughs, A.M., Aravind, L., Whiteley, A.T., Morehouse, B.R.

(2025) Nature 

• PubMed: 41034579 
• DOI: https://doi.org/10.1038/s41586-025-09557-z
• Primary Citation of Related Structures:  
  9MNR, 9PD0


• PubMed Abstract: 
  

  Bacteria combat phage infection using antiphage systems and many systems generate nucleotide-derived second messengers upon infection that activate effector proteins to mediate immunity ¹ . Phages respond with counter-defences that deplete these second messengers, leading to an escalating arms race with the host. Here we outline an antiphage system we call Panoptes that indirectly detects phage infection when phage proteins antagonize the nucleotide-derived second-messenger pool. Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence. Crystal structures show that OptS is a minimal CRISPR polymerase (mCpol) domain, a version of the polymerase domain found in type III CRISPR systems (Cas10). OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2',3'-cyclic diadenosine monophosphate (2',3'-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. Panoptes potently restricted phage replication, but phages that had loss-of-function mutations in anti-cyclic oligonucleotide-based antiphage signalling system (CBASS) protein 2 (Acb2) escaped defence. These findings were unexpected because Acb2 is a nucleotide 'sponge' that antagonizes second-messenger signalling. Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence. These data demonstrate a sophisticated immune strategy that bacteria use to guard their second-messenger pool and turn immune evasion against the virus.

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Organizational Affiliation: 
• Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA.
Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.
Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA.
Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, CA, USA.
Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. [e-mail].
Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA. [e-mail].
Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA. [e-mail].
Institute for Immunology, University of California, Irvine, Irvine, CA, USA. [e-mail].
Center for Virus Research, University of California, Irvine, Irvine, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 60.56 kDa 
• Atom Count: 3,914 
• Modeled Residue Count: 478 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Panoptes OptS minimal CRISPR polymerase (mCpol)	A, B, C, D	131	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: APT92_27075, FXN67_14895, GJJ08_009245, NCTC13443_05031
UniProt
Find proteins for A0A2G9LI54 (Klebsiella pneumoniae) Explore A0A2G9LI54  Go to UniProtKB:  A0A2G9LI54

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APC (Subject of Investigation/LOI)	E [auth A], H [auth B], K [auth C], N [auth D]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C11 H18 N5 O12 P3 CAWZRIXWFRFUQB-IOSLPCCCSA-N
MG	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.270 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.42	α = 90
b = 89.534	β = 90
c = 104.222	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: 2025-09-24 
Deposition Author(s): Dinh, D.M., Morehouse, B.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release
  
• Version 1.1: 2025-10-08
  Changes: Database references