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- EMDB-19048: Complex between the RecA-like Sak4 SSAP and the SaPI2 Stl master ... -

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Basic information

Entry
Database: EMDB / ID: EMD-19048
TitleComplex between the RecA-like Sak4 SSAP and the SaPI2 Stl master regulator
Map data
Sample
  • Complex: Complex between Sak4 SSAP from staphylococcal phage 52A and the SaPI2 Stl master regulator
    • Protein or peptide: ORF016
    • Protein or peptide: Helix-turn-helix XRE family protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsAnnealase / 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 / C18 / Ring
Function / homologyAAA domain / Cro/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 / P-loop containing nucleoside triphosphate hydrolase / Helix-turn-helix XRE family protein / ORF016
Function and homology information
Biological speciesStaphylococcus aureus (bacteria) / Staphylococcus phage 52A (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsDebiasi-Anders G / Mir-Sanchis I
Funding support Sweden, 1 items
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
DepositionDec 6, 2023-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19048.png

Downloads & links

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Map

FileDownload / File: emd_19048.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 500 pix.
= 373. Å		0.75 Å/pix.
x 500 pix.
= 373. Å		0.75 Å/pix.
x 500 pix.
= 373. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.746 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.17919694 - 0.36775768
Average (Standard dev.)0.000017884362 (±0.011211461)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 373.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19048_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19048_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between Sak4 SSAP from staphylococcal phage 52A and the S...

EntireName: Complex between Sak4 SSAP from staphylococcal phage 52A and the SaPI2 Stl master regulator
Components
  • Complex: Complex between Sak4 SSAP from staphylococcal phage 52A and the SaPI2 Stl master regulator
    • Protein or peptide: ORF016
    • Protein or peptide: Helix-turn-helix XRE family protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: Complex between Sak4 SSAP from staphylococcal phage 52A and the S...

SupramoleculeName: Complex between Sak4 SSAP from staphylococcal phage 52A and the SaPI2 Stl master regulator
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: ORF016

MacromoleculeName: ORF016 / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 52A (virus)
Molecular weightTheoretical: 31.653682 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MTEKTNQDVD ILTQLGVKDI SKQNANKFYK FAIYGKFGTG KTTFLTKDNN ALVLDINEDG TTVTEDGAV VQIKNYKHFS AVIKMLPKII EQLRENGKQI DVVVIETIQK LRDITMDDIM DGKSKKPTFN DWGECATRIV S IYRYISKL ...String:
MGSSHHHHHH SSGLVPRGSH MTEKTNQDVD ILTQLGVKDI SKQNANKFYK FAIYGKFGTG KTTFLTKDNN ALVLDINEDG TTVTEDGAV VQIKNYKHFS AVIKMLPKII EQLRENGKQI DVVVIETIQK LRDITMDDIM DGKSKKPTFN DWGECATRIV S IYRYISKL QEHYQFHLAI SGHEGINKDK DDEGSTINPT ITIEAQDQIK KAVISQSDVL ARMTIEEHEQ DGEKTYQYVL NA EPSNLFE TKIRHSSNIK INNKRFINPS INDVVQAIRN GN

UniProtKB: ORF016

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Macromolecule #2: Helix-turn-helix XRE family protein

MacromoleculeName: Helix-turn-helix XRE family protein / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria) / Strain: RN3984
Molecular weightTheoretical: 27.189562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIRNRLSELL SERGLKISRV AKDVKIARSS LTSMAQNDSE MIRYDAIDKL CSYLHISPSE FFEHNPINFD FTFDEEPNYK INDVFEGFE VTANITHAFS IENFDFEILV DVELDNRQKL NFDLDVSYKE TEKITNSQHR FIFTIKNEDE NIGLKKYVDS L SAGLKNLL ...String:
MIRNRLSELL SERGLKISRV AKDVKIARSS LTSMAQNDSE MIRYDAIDKL CSYLHISPSE FFEHNPINFD FTFDEEPNYK INDVFEGFE VTANITHAFS IENFDFEILV DVELDNRQKL NFDLDVSYKE TEKITNSQHR FIFTIKNEDE NIGLKKYVDS L SAGLKNLL FKKINQKLSG YVSEIIVKNI DDIEELFPNK GEKSTTLHKE ILQTDSRLSS DIFKEYLEHH HHHH

UniProtKB: Helix-turn-helix XRE family protein

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 16 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
20.0 mMTrisTris
1.0 mMDTTDTT
2.0 mMATPySATPyS

Details: 100mM NaCl, 20mM Tris-HCl pH 7.0, 1mM DTT and 2mM ATPyS. No metal was added.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse sample.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 1301 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 190000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Details: Symmetry-expanded to D1, doubling the particle stack, from 141863 to 283726 particles.
Number images used: 141863
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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