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- EMDB-66345: cryo-electron microscopy structure of Dandelion -

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Basic information

Entry
Database: EMDB / ID: EMD-66345
Titlecryo-electron microscopy structure of Dandelion
Map data
Sample
  • Complex: Dandelion
    • Protein or peptide: Dandelion
Keywordsdodecamer / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsYu Y / Chen Q / Tang Y
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66345.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 512 pix.
= 435.2 Å		0.85 Å/pix.
x 512 pix.
= 435.2 Å		0.85 Å/pix.
x 512 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0225
Minimum - Maximum-0.0017463381 - 2.0722091
Average (Standard dev.)0.0011420663 (±0.024621312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66345_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_66345_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dandelion

EntireName: Dandelion
Components
  • Complex: Dandelion
    • Protein or peptide: Dandelion

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Supramolecule #1: Dandelion

SupramoleculeName: Dandelion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Dandelion

MacromoleculeName: Dandelion / type: protein_or_peptide / ID: 1 / Details: Dandelion / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 53.749062 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GASGSMDVRI FSLESQKSKI YDRRTRKYFE EVYKSYANGC YRSATVMLWS VVVCDIIFKL QELRDVHNDA VAEKILLEIE ALQNDDPYS PKWEKELIKR VFERTQLLDT ASNHKVLLIQ KHRHLSAHPV ISDEDTLFEP TQEMIRSDIR NSIEVILSKP P FMSQKILS ...String:
GASGSMDVRI FSLESQKSKI YDRRTRKYFE EVYKSYANGC YRSATVMLWS VVVCDIIFKL QELRDVHNDA VAEKILLEIE ALQNDDPYS PKWEKELIKR VFERTQLLDT ASNHKVLLIQ KHRHLSAHPV ISDEDTLFEP TQEMIRSDIR NSIEVILSKP P FMSQKILS TFVADLEKVK DLFPSDNALK KYLDVKYFKS LNKEVLVKIF KGLWKFSFRS EEAKPLENRE INIRAMKLIF EK DRQAMVD SVKAETAYYS NISNNHDAIK ALIEFISMEK EIYNALDDSV KELIKPIIKD NISYFGIAFF ISESPEEHIN RVT KRISEK YYKKYGDNGN FLNQQHLAIF KNVCSELGLE SEYRDFGIAC FINSADFERA DIYFDRFIDK DLANYSSEQM LTLL EGANK NNQCYWRNRS RNGNDSIRIL KAAKNKLPDG FDFSKYDNLP VDKIDHVLEE DVGER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 55.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.966 µm / Nominal defocus min: 0.404 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 70976
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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