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- EMDB-17821: Sak Single Strand Annealing Protein from Staphylococcal Bacteriop... -

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Basic information

Entry
Database: EMDB / ID: EMD-17821
TitleSak Single Strand Annealing Protein from Staphylococcal Bacteriophage 80a - dCTD
Map data
Sample
  • Complex: 18-mer ring cryoEM structure of the 80a-Sak NTD in apo state
    • Protein or peptide: Topoisomerase
  • Ligand: water
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 / homologySingle-strand annealing protein SAK3 / Protein of unknown function (DUF1071) / isomerase activity / Topoisomerase
Function and homology information
Biological speciesStaphylococcus phage 80alpha (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 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
DepositionJul 10, 2023-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17821.png

Downloads & links

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Map

FileDownload / File: emd_17821.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 298.4 Å		0.75 Å/pix.
x 400 pix.
= 298.4 Å		0.75 Å/pix.
x 400 pix.
= 298.4 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: 0.085
Minimum - Maximum-0.43517983 - 0.83766866
Average (Standard dev.)0.00014438934 (±0.019485127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 298.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17821_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17821_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17821_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : 18-mer ring cryoEM structure of the 80a-Sak NTD in apo state

EntireName: 18-mer ring cryoEM structure of the 80a-Sak NTD in apo state
Components
  • Complex: 18-mer ring cryoEM structure of the 80a-Sak NTD in apo state
    • Protein or peptide: Topoisomerase
  • Ligand: water

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Supramolecule #1: 18-mer ring cryoEM structure of the 80a-Sak NTD in apo state

SupramoleculeName: 18-mer ring cryoEM structure of the 80a-Sak NTD in apo state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 460 KDa

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Macromolecule #1: Topoisomerase

MacromoleculeName: Topoisomerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Molecular weightTheoretical: 19.417621 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKHHHHHHPM SDYDIPTTEN LYFQGAMGMT EQTLFEQLNS KNVNDHTEQK NGLTYLAWSY AHQELKKIDP NYTVKVHEFP HPDINTENY FVPYLATPEG YFVQVSVTVK DSTETEWLPV LDFRNKSLAK GSATTFDINK AQKRCFVKAS ALHGLGLYIY N GEELPSAS D

UniProtKB: Topoisomerase

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 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
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: 4344 / Average exposure time: 2.99 sec. / 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: 2.9 µm / Nominal defocus min: 1.6 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: C18 (18 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Software - details: Local refinement job after symmetry expansion
Details: Symmetry expanded to C18, multiplying the stack by 18, from 75703 to 1365300 particles.
Number images used: 75703
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 - Residue range: 1-141 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: AlphaFold prediction was done locally. CTD residues of the full-length AlphaFold prediction were deleted before fiting with ChimeraX.
DetailsFitting of the truncated AlphaFold prediction was done with ChimeraX and then subjected to real space refinement in PHENIX. The output was then repeatedly adjusted with Coot and verified in PHENIX.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8pq8:
Sak Single Strand Annealing Protein from Staphylococcal Bacteriophage 80a - dCTD

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