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- PDB-9wxf: cryo-electron microscopy structure of Dandelion -

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Basic information

Entry
Database: PDB / ID: 9wxf
Titlecryo-electron microscopy structure of Dandelion
ComponentsDandelion
KeywordsIMMUNE SYSTEM / dodecamer
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsYu, Y. / Chen, Q. / Tang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Cell / Year: 2026
Title: Oligomer disassembly activates an HEPN-containing bacterial defense system.
Authors: Yiwen Tang / Ting Liu / Chao Xiong / Qiang Chen / Yamei Yu /
Abstract: The evolutionary arms race between bacteria and phages has driven the diversification of prokaryotic antiviral defense mechanisms, with nucleic acid degradation emerging as a central strategy. Here, ...The evolutionary arms race between bacteria and phages has driven the diversification of prokaryotic antiviral defense mechanisms, with nucleic acid degradation emerging as a central strategy. Here, we investigate a Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) domain-containing defense system from Escherichia coli that mediates RNase-dependent abortive infection. In contrast to canonical immune systems, where oligomerization triggers signaling, this system adopts a dodecameric autoinhibited architecture, with RNase activity unleashed upon oligomer dissociation. This activation mechanism is reminiscent of the dispersal of dandelion seeds, and we therefore term this defense system "Dandelion." We further identify the phage single-stranded DNA-binding (SSB) protein as a trigger for the Dandelion system, and phylogenetic analysis of SSB proteins uncovers the specificity underlying phage resistance. Our findings reveal a counterintuitive paradigm in bacterial immunity-‌oligomer disassembly as an activation switch, which challenges the long-standing dogma that protein oligomerization activates immune signaling.
History
DepositionSep 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 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
A: Dandelion
B: Dandelion
C: Dandelion
D: Dandelion
E: Dandelion
F: Dandelion
G: Dandelion
H: Dandelion
I: Dandelion
J: Dandelion
K: Dandelion
L: Dandelion


Theoretical massNumber of molelcules
Total (without water)644,98912
Polymers644,98912
Non-polymers00
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
Dandelion


Mass: 53749.062 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Dandelion / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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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: Dandelion / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4966 nm / Nominal defocus min: 404 nm
Image recordingElectron dose: 55.68 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.15.2_3472model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70976 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00478040
ELECTRON MICROSCOPYf_angle_d0.72140971
ELECTRON MICROSCOPYf_dihedral_angle_d6.57131749
ELECTRON MICROSCOPYf_chiral_restr0.0365780
ELECTRON MICROSCOPYf_plane_restr0.00311378

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