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- PDB-9wwz: Crystal structure of CTD of Dandelion -

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Basic information

Entry
Database: PDB / ID: 9wwz
TitleCrystal structure of CTD of Dandelion
ComponentsDandelion
KeywordsIMMUNE SYSTEM / Dandelion
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.785 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 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dandelion
B: Dandelion


Theoretical massNumber of molelcules
Total (without water)70,5962
Polymers70,5962
Non-polymers00
Water79344
1
A: Dandelion


Theoretical massNumber of molelcules
Total (without water)35,2981
Polymers35,2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dandelion


Theoretical massNumber of molelcules
Total (without water)35,2981
Polymers35,2981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.610, 150.880, 51.339
Angle α, β, γ (deg.)90.00, 90.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dandelion


Mass: 35297.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0% (w/v) PEG 8000, 0.05 M KCl, 0.05 M sodium cacodylate (pH 6.0), 0.5 mM spermine, and 0.5 mM L-argininamide dihydrochloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.785→50.606 Å / Num. obs: 19142 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.984 / Rpim(I) all: 0.112 / Net I/σ(I): 7.7
Reflection shellResolution: 2.79→2.94 Å / Num. unique obs: 2794 / Rpim(I) all: 0.382 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.785→50.606 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 1009 5.27 %
Rwork0.2323 --
obs0.2343 19142 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.785→50.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4734 0 0 44 4778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034826
X-RAY DIFFRACTIONf_angle_d0.6056477
X-RAY DIFFRACTIONf_dihedral_angle_d3.1032955
X-RAY DIFFRACTIONf_chiral_restr0.04686
X-RAY DIFFRACTIONf_plane_restr0.003837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7855-2.93230.3361510.30832577X-RAY DIFFRACTION100
2.9323-3.1160.32931440.28692601X-RAY DIFFRACTION100
3.116-3.35650.27321410.26412616X-RAY DIFFRACTION100
3.3565-3.69420.32261390.24872596X-RAY DIFFRACTION100
3.6942-4.22860.27181420.22122525X-RAY DIFFRACTION96
4.2286-5.32660.26521450.20672574X-RAY DIFFRACTION100
5.3266-50.60.18831470.17972644X-RAY DIFFRACTION100

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