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- EMDB-70609: BtCap14 SAVED domain + 2',3'-cGAMP -

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Basic information

Entry
Database: EMDB / ID: EMD-70609
TitleBtCap14 SAVED domain + 2',3'-cGAMP
Map data
Sample
  • Complex: BtCap14 SAVED domain + 2'3'-cGAMP filament
    • Protein or peptide: SAVED domain-containing protein
  • Ligand: cGAMP
KeywordsSaf-2TM-SAVED / Cap14 / cGAMP / antiphage / ANTIVIRAL PROTEIN
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / SAVED domain-containing protein
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTak U / Hartwick EW / Whiteley AT
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP2AT012346 United States
CitationJournal: Cell Host Microbe / Year: 2026
Title: Bacterial 2',3'-cGAMP activates a SAVED effector to form membrane-disrupting filaments and restrict phage replication.
Authors: Uday Tak / Kate Schinkel / Peace Walth / Jian Wei Tay / Erik W Hartwick / Aaron T Whiteley /
Abstract: Mammalian cells initiate antiviral signaling when cyclic GMP-AMP synthase (cGAS) detects cytoplasmic DNA and synthesizes 2',3'-cyclic GMP-AMP (2',3'-cGAMP), which activates stimulator of interferon ...Mammalian cells initiate antiviral signaling when cyclic GMP-AMP synthase (cGAS) detects cytoplasmic DNA and synthesizes 2',3'-cyclic GMP-AMP (2',3'-cGAMP), which activates stimulator of interferon genes (STING). Similarly, bacteria use cyclic oligonucleotide-based antiphage signaling systems (CBASS) to detect phage using ancestral cGAS/DncV-like nucleotidyltransferases (CD-NTases), but they are not known to use 2',3'-cGAMP. Here, we discover a bacterial CD-NTase that produces 2',3'-cGAMP to activate a Saf-2TM-SMODS-associated fused to various effector domains (SAVED) effector (CD-NTase-associated protein 14 [Cap14]), which initiates membrane disruption to restrict phage replication. Cryo-electron microscopy (cryo-EM) reveals that Cap14 binds 2',3'-cGAMP to form a filament, while electrophysiology suggests that cGAMP activates membrane disruption. Swapping the Cap14 transmembrane domain with a nuclease domain yields a functional chimera that exclusively responds to 2',3'-cGAMP. We hypothesize that other predicted transmembrane effectors in CBASS operons disrupt membranes, and we confirm this by showing that bacterial STING homologs with transmembrane domains restrict phage through membrane disruption. These findings expand our understanding of cGAS-STING-like pathways in bacterial immunity.
History
DepositionMay 13, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70609.png

Downloads & links

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Map

FileDownload / File: emd_70609.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 270 pix.
= 261.9 Å		0.97 Å/pix.
x 270 pix.
= 261.9 Å		0.97 Å/pix.
x 270 pix.
= 261.9 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.727427 - 1.3481644
Average (Standard dev.)0.0031535246 (±0.03859011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 261.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70609_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_70609_half_map_2.map
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Sample components

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Entire : BtCap14 SAVED domain + 2'3'-cGAMP filament

EntireName: BtCap14 SAVED domain + 2'3'-cGAMP filament
Components
  • Complex: BtCap14 SAVED domain + 2'3'-cGAMP filament
    • Protein or peptide: SAVED domain-containing protein
  • Ligand: cGAMP

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Supramolecule #1: BtCap14 SAVED domain + 2'3'-cGAMP filament

SupramoleculeName: BtCap14 SAVED domain + 2'3'-cGAMP filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: Bt407

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Macromolecule #1: SAVED domain-containing protein

MacromoleculeName: SAVED domain-containing protein / type: protein_or_peptide / ID: 1 / Details: Full length BtCap14-GS-6xhis / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: Bt407
Molecular weightTheoretical: 42.939117 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNIVTFGIIL VVTTIIMIIL YAFNRTKGVE TFGGHTFISF GLGLITGSFG TLVDKIHSIV IAIIKVTNDK TQAKTLTDAT DVNYIQLVT GIAFVALGIW FIYKLKNRIY ILNINGYADH RIENNQKSLG LNEFDFKERE IEFIQRFKKA QRNATEQDVI P EITEELVP ...String:
MNIVTFGIIL VVTTIIMIIL YAFNRTKGVE TFGGHTFISF GLGLITGSFG TLVDKIHSIV IAIIKVTNDK TQAKTLTDAT DVNYIQLVT GIAFVALGIW FIYKLKNRIY ILNINGYADH RIENNQKSLG LNEFDFKERE IEFIQRFKKA QRNATEQDVI P EITEELVP KLEAFKNESR KVKRGYTGIA PIPLILYAGK ILDGHEINHF YERNKFTQQY YKLDKSKKNY EKLNLQTNLQ AL ANMQVTE AVLKVSITFD ISTQDTSQFG NIPVVELKVD APNENLVSGK DQLDSYVKKV YDTIRDIKTS NHAIQRIHLL ISS QSCVPF ELGRLLDDTS MPEIISYQYE NPTYRWGLIV NKNNKGTFIT APGSHHHHHH

UniProtKB: SAVED domain-containing protein

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Macromolecule #2: cGAMP

MacromoleculeName: cGAMP / type: ligand / ID: 2 / Number of copies: 6 / Formula: 1SY
Molecular weightTheoretical: 674.411 Da
Chemical component information

ChemComp-1SY:
cGAMP

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: de novo generated in Phenix
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 117999
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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