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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: 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 JW / Hartwick EW / Whiteley AT
History
DepositionMay 13, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 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
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70609_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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