8UX9 | pdb_00008ux9

Asymmetric unit of the PARIS Immune Complex at 3.2 Angstrom Resolution

• PDB DOI: https://doi.org/10.2210/pdb8UX9/pdb
• EM Map EMD-42719: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli B185
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-09 Released: 2024-09-18 
• Deposition Author(s): Burman, N.B., Henriques, W., Wilkinson, R., Graham, A., Wiedenheft, B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

A virally encoded tRNA neutralizes the PARIS antiviral defence system.

Burman, N., Belukhina, S., Depardieu, F., Wilkinson, R.A., Skutel, M., Santiago-Frangos, A., Graham, A.B., Livenskyi, A., Chechenina, A., Morozova, N., Zahl, T., Henriques, W.S., Buyukyoruk, M., Rouillon, C., Saudemont, B., Shyrokova, L., Kurata, T., Hauryliuk, V., Severinov, K., Groseille, J., Thierry, A., Koszul, R., Tesson, F., Bernheim, A., Bikard, D., Wiedenheft, B., Isaev, A.

(2024) Nature 634: 424-431

• PubMed: 39111359 
• DOI: https://doi.org/10.1038/s41586-024-07874-3
• Primary Citation Related Structures: 
  8UX9


• PubMed Abstract: 
  

  Viruses compete with each other for limited cellular resources, and some deliver defence mechanisms that protect the host from competing genetic parasites ¹ . The phage antirestriction induced system (PARIS) is a defence system, often encoded in viral genomes, that is composed of a 55 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB) ² . However, the mechanism by which AriA and AriB function in phage defence is unknown. Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex. We use cryo-electron microscopy to determine the structure of this complex, thereby explaining how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving host lysine transfer RNA. Phage T5 subverts PARIS immunity through expression of a lysine transfer RNA variant that is not cleaved by PARIS, thereby restoring viral infection. Collectively, these data explain how AriA functions as an ATP-dependent sensor that detects viral proteins and activates the AriB toxin. PARIS is one of an emerging set of immune systems that form macromolecular complexes for the recognition of foreign proteins, rather than foreign nucleic acids ³ .

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Organizational Affiliation: 
• Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
The Center for Molecular and Cellular Biology, Moscow, Russia.
Synthetic Biology, Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Paris, France.
Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
Peter the Great St Petersburg State Polytechnic University, St. Petersburg, Russia.
Department of Experimental Medical Science, Lund University, Lund, Sweden.
Virus Centre, Lund University, Lund, Sweden.
Science for Life Laboratory, Lund, Sweden.
Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Unité Régulation Spatiale des Génomes, Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Paris, France.
Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France.
Collège Doctoral, Sorbonne Université, Paris, France.
Molecular Diversity of Microbes, Institut Pasteur, CNRS UMR3525, Université Paris Cité, Paris, France.
Synthetic Biology, Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Paris, France. [e-mail].
Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA. [e-mail].
The Center for Molecular and Cellular Biology, Moscow, Russia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 143.54 kDa 
• Atom Count: 7,783 
• Modeled Residue Count: 1,104 
• Deposited Residue Count: 1,244 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AriB	A	316	Escherichia coli B185	Mutation(s): 0  Gene Names: ECDG_03486

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AriA	B, C	464	Escherichia coli B185	Mutation(s): 0  Gene Names: ECDG_03487

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	D [auth B], E [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3.1
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-18 
Deposition Author(s): Burman, N.B., Henriques, W., Wilkinson, R., Graham, A., Wiedenheft, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM134867

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release
  
• Version 1.1: 2025-04-02
  Changes: Data collection, Database references, Structure summary