8QE9 | pdb_00008qe9

Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulator


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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

Phage parasites targeting phage homologous recombinases provide antiviral immunity.

Debiasi-Anders, G.Qiao, C.Salim, A.Li, N.Mir-Sanchis, I.

(2025) Nat Commun 16: 1889-1889

  • DOI: https://doi.org/10.1038/s41467-025-57156-3
  • Primary Citation of Related Structures:  
    8PQ8, 8Q86, 8QE9, 8RC5

  • PubMed Abstract: 

    Bacteria often carry multiple genes encoding anti-phage defense systems, clustered in defense islands and phage satellites. Various unrelated anti-phage defense systems target phage-encoded homologous recombinases (HRs) through unclear mechanisms. Here, we show that the phage satellite SaPI2, which does not encode orthodox anti-phage defense systems, provides antiviral immunity mediated by Stl2, the SaPI2-encoded transcriptional repressor. Stl2 targets and inhibits phage-encoded HRs, including Sak and Sak4, two HRs from the Rad52-like and Rad51-like superfamilies. Remarkably, apo Stl2 forms a collar of dimers oligomerizing as closed rings and as filaments, mimicking the quaternary structure of its targets. Stl2 decorates both Sak rings and Sak4 filaments. The oligomerization of Stl2 as a collar of dimers is necessary for its inhibitory activity both in vitro and in vivo. Our results shed light on the mechanisms underlying antiviral immunity against phages carrying divergent HRs.


  • Organizational Affiliation
    • Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF1071 domain-containing protein206Staphylococcus phage 80alphaMutation(s): 0 
Gene Names: HMPREF0776_1852
UniProt
Find proteins for A0A0E1X975 (Staphylococcus aureus subsp. aureus MN8)
Explore A0A0E1X975 
Go to UniProtKB:  A0A0E1X975
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E1X975
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Helix-turn-helix XRE family protein233Staphylococcus aureusMutation(s): 0 
Gene Names: stl
UniProt
Find proteins for A0FIL5 (Staphylococcus aureus)
Explore A0FIL5 
Go to UniProtKB:  A0FIL5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0FIL5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.20.1
MODEL REFINEMENTCoot0.9.8.4 EL

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Data collection, Refinement description