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- EMDB-18346: Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulator -

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Basic information

Entry
Database: EMDB / ID: EMD-18346
TitleComplex between the 80a-Sak SSAP and the SaPI2 Stl master regulator
Map data
Sample
  • Complex: Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulator
    • Complex: 80a-Sak SSAP
      • Protein or peptide: DUF1071 domain-containing protein
    • Complex: SaPI2 Stl master regulator
      • Protein or peptide: Helix-turn-helix XRE family protein
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 / Ring / Transcription / Transcriptonal regulator / GENE REGULATION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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
DepositionAug 30, 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_18346.png

Downloads & links

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Map

FileDownload / File: emd_18346.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.)
0.7 Å/pix.
x 500 pix.
= 352. Å		0.7 Å/pix.
x 500 pix.
= 352. Å		0.7 Å/pix.
x 500 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.704 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.044499233 - 0.15852916
Average (Standard dev.)0.000855342 (±0.010157433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18346_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18346_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18346_half_map_2.map
Projections & Slices
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Sample components

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

EntireName: Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulator
Components
  • Complex: Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulator
    • Complex: 80a-Sak SSAP
      • Protein or peptide: DUF1071 domain-containing protein
    • Complex: SaPI2 Stl master regulator
      • Protein or peptide: Helix-turn-helix XRE family protein

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Supramolecule #1: Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulator

SupramoleculeName: Complex between the 80a-Sak SSAP and the SaPI2 Stl master regulator
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 1.6 MDa

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Supramolecule #2: 80a-Sak SSAP

SupramoleculeName: 80a-Sak SSAP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus phage 80alpha (virus)

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Supramolecule #3: SaPI2 Stl master regulator

SupramoleculeName: SaPI2 Stl master regulator / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: DUF1071 domain-containing protein

MacromoleculeName: DUF1071 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 23.63935 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: TEQTLFEQLN SKNVNDHTEQ KNGLTYLAWS YAHQELKKID PNYTVKVHEF PHPDINTENY FVPYLATPEG YFVQVSVTVK DSTETEWLP VLDFRNKSLA KGSATTFDIN KAQKRCFVKA SALHGLGLYI YNGEELPSAS DNDITELEER INQFVNLSQE K GRDATIDK ...String:
TEQTLFEQLN SKNVNDHTEQ KNGLTYLAWS YAHQELKKID PNYTVKVHEF PHPDINTENY FVPYLATPEG YFVQVSVTVK DSTETEWLP VLDFRNKSLA KGSATTFDIN KAQKRCFVKA SALHGLGLYI YNGEELPSAS DNDITELEER INQFVNLSQE K GRDATIDK TMRWLKISNI NKLSQKQIAE AHQKLDAGLK QLDSEEKQ

UniProtKB: UNIPROTKB: A0A0E1VL05

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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: 30 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria) / Strain: RN3984
Molecular weightTheoretical: 27.148473 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGIRNRLSEL LSERGLKISR VAKDVKIARS SLTSMAQNDS EMIRYDAIDK LCSYLHISPS EFFEHNPINF DFTFDEEPNY KINDVFEGF EVTANITHAF SIENFDFEIL VDVELDNRQK LNFDLDVSYK ETEKITNSQH RFIFTIKNED ENIGLKKYVD S LSAGLKNL ...String:
MGIRNRLSEL LSERGLKISR VAKDVKIARS SLTSMAQNDS EMIRYDAIDK LCSYLHISPS EFFEHNPINF DFTFDEEPNY KINDVFEGF EVTANITHAF SIENFDFEIL VDVELDNRQK LNFDLDVSYK ETEKITNSQH RFIFTIKNED ENIGLKKYVD S LSAGLKNL LFKKINQKLS GYVSEIIVKN IDDIEELFPN KGEKSTTLHK EILQTDSRLS SDIFKEYGSH HHHHH

UniProtKB: Helix-turn-helix XRE family protein

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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

BufferpH: 8.1
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl pH 7.6
100.0 mMNaClSodium Chloride
1.0 mMDTTDithiothreitol

Details: 20mM Tris-HCl pH 7.6, 100mM NaCl, 1mM DTT
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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Details: Final particle set was symmetry-expanded to D1, multiplying it by 2 to 416444 particles.
Number images used: 208222
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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Atomic model buiding 1

Initial modelChain - Chain ID: A / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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