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- PDB-9om7: BtCap14 SAVED domain + 2',3'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 9om7
TitleBtCap14 SAVED domain + 2',3'-cGAMP
ComponentsSAVED domain-containing protein
KeywordsANTIVIRAL PROTEIN / Saf-2TM-SAVED / Cap14 / cGAMP / antiphage
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / cGAMP / SAVED domain-containing protein
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTak, U. / Hartwick, E.W. / Whiteley, A.T.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: SAVED domain-containing protein
E: SAVED domain-containing protein
B: SAVED domain-containing protein
D: SAVED domain-containing protein
A: SAVED domain-containing protein
C: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,68112
Polymers257,6356
Non-polymers4,0466
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
SAVED domain-containing protein


Mass: 42939.117 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Full length BtCap14-GS-6xhis / Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: Bt407 / Gene: FLM80_14620 / Plasmid: pAW1517 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0AAP4Q8A7
#2: Chemical
ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN
Sequence detailsThis sequence may be found at NCBI with accession code WP_001028553.1.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BtCap14 SAVED domain + 2'3'-cGAMP filament / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: Bt407
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43(DE3) / Plasmid: pAW1517
Buffer solutionpH: 7.2
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117999 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213406
ELECTRON MICROSCOPYf_angle_d0.4918179
ELECTRON MICROSCOPYf_dihedral_angle_d22.0561801
ELECTRON MICROSCOPYf_chiral_restr0.0412017
ELECTRON MICROSCOPYf_plane_restr0.0032312

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