8UX9 | pdb_00008ux9

Asymmetric unit of the PARIS Immune Complex at 3.2 Angstrom Resolution


Experimental Data Snapshot

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

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


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41586-024-07874-3
  • Primary Citation of 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 .


  • Organizational Affiliation

    Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AriB316Escherichia coli B185Mutation(s): 0 
Gene Names: ECDG_03486
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AriA
B, C
464Escherichia coli B185Mutation(s): 0 
Gene Names: ECDG_03487
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.3.1
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM134867

Revision History  (Full details and data files)

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