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- EMDB-66158: Structure of 3TM-SAVED Filament bound to 2'3'-cGAMP -

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Basic information

Entry
Database: EMDB / ID: EMD-66158
TitleStructure of 3TM-SAVED Filament bound to 2'3'-cGAMP
Map data
Sample
  • Complex: 3TM-SAVED Filament
    • Protein or peptide: 2-methylthioadenine synthetase
  • Ligand: cGAMP
KeywordsSAVED / IMMUNE SYSTEM
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / 2-methylthioadenine synthetase
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGao YN
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2026
Title: 2'3'-cGAMP-induced membrane shearing promotes broad antiphage immunity.
Authors: Yina Gao / Zhaolong Li / Yufei Zhou / Weimin Li / Quanjin Li / Jingge Wang / Miao Shi / Feng Ye / Chunqiu Zhao / Songqing Liu / Qiuyao Jiang / Yun Zhu / Fei Sun / Ang Gao / Pu Gao /
Abstract: Cyclic-oligonucleotide-based anti-phage signaling system (CBASS), a central prokaryotic antiviral strategy and evolutionary ancestor of the mammalian cyclic GMP-AMP synthase (cGAS)-stimulator of ...Cyclic-oligonucleotide-based anti-phage signaling system (CBASS), a central prokaryotic antiviral strategy and evolutionary ancestor of the mammalian cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, relies on cyclic-nucleotide-activated effectors to elicit immunity. The most prevalent effectors are transmembrane (TM) proteins, yet their mechanisms remain unknown. Here, we show how a representative three transmembrane (3TM)-SMODS-associated fused to various effector domains (SAVED) effector couples ligand sensing to membrane disruption. Upon binding 2'3'-cyclic GMP-AMP (cGAMP)-synthesized by bacterial cGAS/DncV-like nucleotidyltransferase (CD-NTase) with features resembling mammalian cGAS-3TM-SAVED assembles stepwise from an apo monomer through a transient dimer into extended filaments. Filament assembly employs 2'3'-cGAMP as molecular glue linking SAVED domains and reorients TM helices and amphipathic hairpins into vertically offset arrays. Both arrays bear opposing hydrophobic and hydrophilic faces, thereby driving vertical lipid shearing. This shearing generates a linear pore array that permeabilizes membranes and triggers cell death. These findings uncover the long-missing mechanism of CBASS TM effectors and establish vertical membrane shearing as an unrecognized principle of membrane disruption across domains of life.
History
DepositionSep 10, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66158.png

Downloads & links

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Map

FileDownload / File: emd_66158.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.209
Minimum - Maximum-1.668678 - 2.643716
Average (Standard dev.)0.0040342677 (±0.08391089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66158_half_map_1.map
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Half map: #2

Fileemd_66158_half_map_2.map
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Sample components

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Entire : 3TM-SAVED Filament

EntireName: 3TM-SAVED Filament
Components
  • Complex: 3TM-SAVED Filament
    • Protein or peptide: 2-methylthioadenine synthetase
  • Ligand: cGAMP

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Supramolecule #1: 3TM-SAVED Filament

SupramoleculeName: 3TM-SAVED Filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacillus thuringiensis (bacteria)

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Macromolecule #1: 2-methylthioadenine synthetase

MacromoleculeName: 2-methylthioadenine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thuringiensis (bacteria)
Molecular weightTheoretical: 41.98116 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNIVTFGIIL VVTTIIMIIL YAFNRTKGVE TFGGHTFISF GLGLITGSFG TLVDKIHSIV IAIIKVTNDK TQAKTLTDAT DVNYIQLVT GVAFVALGIW FIYKLKNRIY ILNINGYADH RIENNQKSLG LNEFDFKERE IEFVKRFTKA QDNSTEQNVV P EIIEELVF ...String:
MNIVTFGIIL VVTTIIMIIL YAFNRTKGVE TFGGHTFISF GLGLITGSFG TLVDKIHSIV IAIIKVTNDK TQAKTLTDAT DVNYIQLVT GVAFVALGIW FIYKLKNRIY ILNINGYADH RIENNQKSLG LNEFDFKERE IEFVKRFTKA QDNSTEQNVV P EIIEELVF KIEAFKNEST NVKRGYTGIA PIPFILYAGK LFNGHKINHF YERNKLKQDY YKLANKKKNF EELTLQTNLQ AL SSTSATE AILKVSLTFD ISTHDTSQFG SNVPVVDLKV DETKENIIQG KDQLEEYVKV VYETIRKINQ SNPSIQRVHL LIA SQSCLP FELGKLLDDT SMPEVISYHF VNPRYKWGII LNKHNKGTFI TAP

UniProtKB: 2-methylthioadenine synthetase

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 402153
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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