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- EMDB-18248: Trimer of the dimeric SaPI2 Stl transcriptional regulator -

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Basic information

Entry
Database: EMDB / ID: EMD-18248
TitleTrimer of the dimeric SaPI2 Stl transcriptional regulator
Map data
Sample
  • Organelle or cellular component: Trimer of the dimeric SaPI2 Stl transcriptional regulator
    • Protein or peptide: Helix-turn-helix XRE family protein
  • Ligand: water
KeywordsTranscriptional regulator / Stl / Staphylococcus aureus Pathogenicity Island / SaPI / SaPI2 / Phage-inducible chromosomal island / PICI / PICIs / transcriptional repressor / transcription regulator / repressor / DNA-binding / DNA BINDING PROTEIN
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 aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsQiao C / Debiasi-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 18, 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_18248.png

Downloads & links

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Map

FileDownload / File: emd_18248.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesX (Sec.)Y (Row.)Z (Col.)
0.75 Å/pix.
x 300 pix.
= 223.8 Å		0.75 Å/pix.
x 300 pix.
= 223.8 Å		0.75 Å/pix.
x 300 pix.
= 223.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.746 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0804
Minimum - Maximum-0.6244903 - 0.9734593
Average (Standard dev.)0.0019766453 (±0.028001335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 223.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18248_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_18248_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18248_half_map_2.map
Projections & Slices
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Sample components

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Entire : Trimer of the dimeric SaPI2 Stl transcriptional regulator

EntireName: Trimer of the dimeric SaPI2 Stl transcriptional regulator
Components
  • Organelle or cellular component: Trimer of the dimeric SaPI2 Stl transcriptional regulator
    • Protein or peptide: Helix-turn-helix XRE family protein
  • Ligand: water

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Supramolecule #1: Trimer of the dimeric SaPI2 Stl transcriptional regulator

SupramoleculeName: Trimer of the dimeric SaPI2 Stl transcriptional regulator
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus aureus (bacteria) / Strain: RN3984
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: Helix-turn-helix XRE family protein

MacromoleculeName: Helix-turn-helix XRE family protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 27.189562 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (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 #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 60 / 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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationName
20.0 mMTris
200.0 mMNaCl
0.5 mMEDTA
3.0 mMDTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2000 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 37.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 53 / Number real images: 6233 / Average exposure time: 3.02 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2337415
Startup modelType of model: OTHER / Details: Alphafold structure
Final reconstructionNumber classes used: 4 / Algorithm: ALGEBRAIC (ARTS) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.1) / Number images used: 594605
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC (ver. v4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

xq92


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient
Output model

PDB-8q86:
Trimer of the dimeric SaPI2 Stl transcriptional regulator

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