9WQ3 | pdb_00009wq3

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9WQ3

This is version 1.1 of the entry. See complete history

Literature

2'3'-cGAMP-induced membrane shearing promotes broad antiphage immunity.

Gao, Y.Li, Z.Zhou, Y.Li, W.Li, Q.Wang, J.Shi, M.Ye, F.Zhao, C.Liu, S.Jiang, Q.Zhu, Y.Sun, F.Gao, A.Gao, P.

(2026) Cell 189: 3636-3650.e19

  • DOI: https://doi.org/10.1016/j.cell.2026.03.043
  • Primary Citation Related Structures: 
    9WQ2, 9WQ3

  • PubMed 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 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.


  • Organizational Affiliation
    • State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 255.93 kDa 
  • Atom Count: 16,619 
  • Modeled Residue Count: 2,031 
  • Deposited Residue Count: 2,214 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-methylthioadenine synthetase369Bacillus thuringiensisMutation(s): 0 
Gene Names: CN398_09390
UniProt
Find proteins for A0A9X6VCG9 (Bacillus thuringiensis)
Explore A0A9X6VCG9 
Go to UniProtKB:  A0A9X6VCG9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9X6VCG9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-04-01 
  • Deposition Author(s): Gao, Y.N.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-01
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references