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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: To Be Published
Title: Bacterial 2',3'-cGAMP activates a SAVED effector to form membrane-disrupting filaments and restrict phage replication
Authors: Tak, U. / Schinkel, K. / Walth, P. / Tay, J.W. / Hartwick, E.W. / Whiteley, A.T.
History
DepositionMay 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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