8RC5 | pdb_00008rc5

Complex between the RecA-like Sak4 SSAP and the SaPI2 Stl master regulator

PDB DOI: https://doi.org/10.2210/pdb8RC5/pdb
EM Map EMD-19048: EMDB EMDataResource

Classification: RECOMBINATION
Organism(s): Staphylococcus phage 52A, Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-06 Released: 2025-03-05
Deposition Author(s): Debiasi-Anders, G., Mir-Sanchis, I.
Funding Organization(s): Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 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

PubMed: 39987160 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-57156-3
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 1,067.55 kDa
Atom Count: 64,360
Modeled Residue Count: 7,866
Deposited Residue Count: 9,198
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF016	A [auth 1A] BA [auth 4G] CA [auth 1H] D [auth 4A] E [auth 1B] A [auth 1A], BA [auth 4G], CA [auth 1H], D [auth 4A], E [auth 1B], FA [auth 4H], GA [auth 1I], H [auth 4B], I [auth 1C], JA [auth 4I], L [auth 4C], M [auth 1D], P [auth 4D], Q [auth 1E], T [auth 4E], U [auth 1F], X [auth 4F], Y [auth 1G]	279	Staphylococcus phage 52A	Mutation(s): 0
UniProt
Find proteins for Q4ZAS5 (Staphylococcus phage 52A) Explore Q4ZAS5 Go to UniProtKB: Q4ZAS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4ZAS5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Helix-turn-helix XRE family protein	AA [auth 3G] B [auth 2A] C [auth 3A] DA [auth 2H] EA [auth 3H] AA [auth 3G], B [auth 2A], C [auth 3A], DA [auth 2H], EA [auth 3H], F [auth 2B], G [auth 3B], HA [auth 2I], IA [auth 3I], J [auth 2C], K [auth 3C], N [auth 2D], O [auth 3D], R [auth 2E], S [auth 3E], V [auth 2F], W [auth 3F], Z [auth 2G]	232	Staphylococcus aureus	Mutation(s): 0 Gene Names: stl
UniProt
Find proteins for A0FIL5 (Staphylococcus aureus) Explore A0FIL5 Go to UniProtKB: A0FIL5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0FIL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download:Ideal Coordinates CCD File SDF format, chain KA [auth 4A] SDF format, chain LA [auth 1B] SDF format, chain MA [auth 4B] SDF format, chain NA [auth 1C] SDF format, chain OA [auth 4C] SDF format, chain PA [auth 1D] SDF format, chain QA [auth 4D] SDF format, chain RA [auth 1E] SDF format, chain SA [auth 4E] SDF format, chain TA [auth 1F] SDF format, chain UA [auth 4F] SDF format, chain VA [auth 1G] SDF format, chain WA [auth 4G] SDF format, chain XA [auth 1H] SDF format, chain YA [auth 4H] SDF format, chain ZA [auth 1I] MOL2 format, chain KA [auth 4A] MOL2 format, chain LA [auth 1B] MOL2 format, chain MA [auth 4B] MOL2 format, chain NA [auth 1C] MOL2 format, chain OA [auth 4C] MOL2 format, chain PA [auth 1D] MOL2 format, chain QA [auth 4D] MOL2 format, chain RA [auth 1E] MOL2 format, chain SA [auth 4E] MOL2 format, chain TA [auth 1F] MOL2 format, chain UA [auth 4F] MOL2 format, chain VA [auth 1G] MOL2 format, chain WA [auth 4G] MOL2 format, chain XA [auth 1H] MOL2 format, chain YA [auth 4H] MOL2 format, chain ZA [auth 1I] mmCIF format, chain KA [auth 4A] mmCIF format, chain LA [auth 1B] mmCIF format, chain MA [auth 4B] mmCIF format, chain NA [auth 1C] mmCIF format, chain OA [auth 4C] mmCIF format, chain PA [auth 1D] mmCIF format, chain QA [auth 4D] mmCIF format, chain RA [auth 1E] mmCIF format, chain SA [auth 4E] mmCIF format, chain TA [auth 1F] mmCIF format, chain UA [auth 4F] mmCIF format, chain VA [auth 1G] mmCIF format, chain WA [auth 4G] mmCIF format, chain XA [auth 1H] mmCIF format, chain YA [auth 4H] mmCIF format, chain ZA [auth 1I]	KA [auth 4A] LA [auth 1B] MA [auth 4B] NA [auth 1C] OA [auth 4C] KA [auth 4A], LA [auth 1B], MA [auth 4B], NA [auth 1C], OA [auth 4C], PA [auth 1D], QA [auth 4D], RA [auth 1E], SA [auth 4E], TA [auth 1F], UA [auth 4F], VA [auth 1G], WA [auth 4G], XA [auth 1H], YA [auth 4H], ZA [auth 1I]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain KA [auth 4A] Focus chain LA [auth 1B] Focus chain MA [auth 4B] Focus chain NA [auth 1C] Focus chain OA [auth 4C] Focus chain PA [auth 1D] Focus chain QA [auth 4D] Focus chain RA [auth 1E] Focus chain SA [auth 4E] Focus chain TA [auth 1F] Focus chain UA [auth 4F] Focus chain VA [auth 1G] Focus chain WA [auth 4G] Focus chain XA [auth 1H] Focus chain YA [auth 4H] Focus chain ZA [auth 1I] Interactions & Density Focus chain KA [auth 4A] Focus chain LA [auth 1B] Focus chain MA [auth 4B] Focus chain NA [auth 1C] Focus chain OA [auth 4C] Focus chain PA [auth 1D] Focus chain QA [auth 4D] Focus chain RA [auth 1E] Focus chain SA [auth 4E] Focus chain TA [auth 1F] Focus chain UA [auth 4F] Focus chain VA [auth 1G] Focus chain WA [auth 4G] Focus chain XA [auth 1H] Focus chain YA [auth 4H] Focus chain ZA [auth 1I]