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- PDB-8qe9: Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulator -

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Basic information

Entry
Database: PDB / ID: 8qe9
TitleComplex between the 80a-Sak SSAP and the SaPI2 Stl master regulator
Components
  • DUF1071 domain-containing protein
  • Helix-turn-helix XRE family protein
KeywordsGENE REGULATION / Annealase / SSAP / Single Strand Annealing / Single Strand Binding / Recombineering / Recombination / SaPI / Bacteriophage / Staphylococcal / Complex / SaPI induction / SaPI2 / Mobile Genetic Element / MGE / PICI / Phage-Inducible Chromosomal Island / Ring / Transcription / Transcriptonal regulator
Function / homologyCro/C1-type HTH DNA-binding domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / : / Helix-turn-helix XRE family protein
Function and homology information
Biological speciesStaphylococcus phage 80alpha (virus)
Staphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsDebiasi-Anders, G. / Mir-Sanchis, I.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2025
Title: Phage parasites targeting phage homologous recombinases provide antiviral immunity.
Authors: Gianluca Debiasi-Anders / Cuncun Qiao / Amrita Salim / Na Li / Ignacio Mir-Sanchis /
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 ...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.
History
DepositionAug 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: DUF1071 domain-containing protein
1B: DUF1071 domain-containing protein
1C: DUF1071 domain-containing protein
1D: DUF1071 domain-containing protein
1E: DUF1071 domain-containing protein
1F: DUF1071 domain-containing protein
1G: DUF1071 domain-containing protein
1H: DUF1071 domain-containing protein
1I: DUF1071 domain-containing protein
1J: DUF1071 domain-containing protein
1K: DUF1071 domain-containing protein
1L: DUF1071 domain-containing protein
1M: DUF1071 domain-containing protein
1N: DUF1071 domain-containing protein
1O: DUF1071 domain-containing protein
1P: DUF1071 domain-containing protein
1Q: DUF1071 domain-containing protein
2A: Helix-turn-helix XRE family protein
2B: Helix-turn-helix XRE family protein
2C: Helix-turn-helix XRE family protein
2D: Helix-turn-helix XRE family protein
2E: Helix-turn-helix XRE family protein
2F: Helix-turn-helix XRE family protein
2G: Helix-turn-helix XRE family protein
2I: Helix-turn-helix XRE family protein
2J: Helix-turn-helix XRE family protein
2L: Helix-turn-helix XRE family protein
2M: Helix-turn-helix XRE family protein
2N: Helix-turn-helix XRE family protein
2O: Helix-turn-helix XRE family protein
2P: Helix-turn-helix XRE family protein
2Q: Helix-turn-helix XRE family protein
3A: Helix-turn-helix XRE family protein
3B: Helix-turn-helix XRE family protein
3C: Helix-turn-helix XRE family protein
3D: Helix-turn-helix XRE family protein
3E: Helix-turn-helix XRE family protein
3F: Helix-turn-helix XRE family protein
3G: Helix-turn-helix XRE family protein
3I: Helix-turn-helix XRE family protein
3J: Helix-turn-helix XRE family protein
3L: Helix-turn-helix XRE family protein
3M: Helix-turn-helix XRE family protein
3N: Helix-turn-helix XRE family protein
3O: Helix-turn-helix XRE family protein
3P: Helix-turn-helix XRE family protein
3Q: Helix-turn-helix XRE family protein
4A: DUF1071 domain-containing protein
4B: DUF1071 domain-containing protein
4C: DUF1071 domain-containing protein
4D: DUF1071 domain-containing protein
4E: DUF1071 domain-containing protein
4F: DUF1071 domain-containing protein
4G: DUF1071 domain-containing protein
4H: DUF1071 domain-containing protein
4I: DUF1071 domain-containing protein
4J: DUF1071 domain-containing protein
4K: DUF1071 domain-containing protein
4L: DUF1071 domain-containing protein
4M: DUF1071 domain-containing protein
4N: DUF1071 domain-containing protein
4O: DUF1071 domain-containing protein
4P: DUF1071 domain-containing protein
4Q: DUF1071 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)1,618,19264
Polymers1,618,19264
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
DUF1071 domain-containing protein


Mass: 23639.350 Da / Num. of mol.: 34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 80alpha (virus) / Gene: HMPREF0776_1852 / Plasmid: pETDuet-1 / Cell (production host): NA / Organ (production host): NA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Tissue (production host): NA / References: UniProt: A0A0E1VL05
#2: Protein ...
Helix-turn-helix XRE family protein


Mass: 27148.473 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN3984 / Gene: stl / Plasmid: pETDuet-1 / Cell (production host): NA / Organ (production host): NA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Tissue (production host): NA / References: UniProt: A0FIL5
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulatorCOMPLEXall0MULTIPLE SOURCES
280a-Sak SSAPCOMPLEX#11RECOMBINANT
3SaPI2 Stl master regulatorCOMPLEX#21RECOMBINANT
Molecular weightValue: 1.6 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Staphylococcus phage 80alpha (virus)2911440
33Staphylococcus aureus (bacteria)1280
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli BL21(DE3) (bacteria)469008
33Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8.1 / Details: 20mM Tris-HCl pH 7.6, 100mM NaCl, 1mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl pH 7.6Tris-HCl1
2100 mMSodium ChlorideNaCl1
31 mMDithiothreitolDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARC4.2.1CTF correction
7UCSF ChimeraX1.6model fitting
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
32PHENIX1.20.1model refinement
33Coot0.9.8.4 ELmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208222
Details: Final particle set was symmetry-expanded to D1, multiplying it by 2 to 416444 particles.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingType: in silico model

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