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- PDB-9tuc: CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - d... -

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Basic information

Entry
Database: PDB / ID: 9tuc
TitleCryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - dimer 5
Components
  • DEAD/DEAH box helicase
  • DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')
  • DNA (5'-D(P*AP*TP*CP*GP*AP*TP*AP*GP*TP*CP*TP*CP*TP*AP*GP*GP*CP*TP*GP*CP*CP*AP*G)-3')
KeywordsHYDROLASE / Bacterial helicase / Druantia / Immune System / NTPase / DNA binding protein / DExH box
Function / homologyPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / :
Function and homology information
Biological speciesEscherichia coli O157:H7 str. EDL933 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsGrass, L.M. / Himpich, S. / Hilal, T. / Loll, B. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2473-2/C4 392923329 Germany
CitationJournal: Cell Rep / Year: 2026
Title: A compact Druantia defense clears phage infections via single-stranded DNA recognition and directional duplex unwinding.
Authors: Stephanie Himpich / Thomas Gaudin / Lena M Grass / Huihui Li / Vu Van Loi / Chao Chen / Eberhard Klauck / Philipp F Popp / Maxilimilian Feussner / Benno Kuropka / Tarek Hilal / Bernhard Loll ...Authors: Stephanie Himpich / Thomas Gaudin / Lena M Grass / Huihui Li / Vu Van Loi / Chao Chen / Eberhard Klauck / Philipp F Popp / Maxilimilian Feussner / Benno Kuropka / Tarek Hilal / Bernhard Loll / Marc Erhardt / Haike Antelmann / Chase L Beisel / Markus C Wahl /
Abstract: Bacteria encode diverse anti-phage defense systems triggered by invader-specific molecular cues. Here, we report that the compact type III-A Druantia system recognizes exposed single-stranded DNA to ...Bacteria encode diverse anti-phage defense systems triggered by invader-specific molecular cues. Here, we report that the compact type III-A Druantia system recognizes exposed single-stranded DNA to block phage replication and drive phage clearance. Using representative systems from Escherichia coli, we show that the two encoded proteins, DruE and DruH, together clear restriction-sensitive or recombination-prone phages without affecting cell growth or viability. DruE dimerizes and engages DNA at exposed single-stranded regions to unwind DNA with 3'-to-5' directionality, resorting to unique molecular lock, wedge, and clamp elements that aid strand separation and processive translocation. DruH is a monomer in isolation and indirectly interacts with DruE and other host proteins under uninfected conditions, with an infection resulting in the dissociation of the complex. Taken together, our results reveal that exposed single-stranded DNA can trigger bacterial immunity through the directional helicase activity of type III-A Druantia.
History
DepositionJan 8, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_DOI / _em_admin.last_update
Revision 1.1Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata
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Revision 1.2Sep 30, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: DEAD/DEAH box helicase
y: DEAD/DEAH box helicase
i: DNA (5'-D(P*AP*TP*CP*GP*AP*TP*AP*GP*TP*CP*TP*CP*TP*AP*GP*GP*CP*TP*GP*CP*CP*AP*G)-3')
g: DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')
G: DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')
I: DNA (5'-D(P*AP*TP*CP*GP*AP*TP*AP*GP*TP*CP*TP*CP*TP*AP*GP*GP*CP*TP*GP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)513,55117
Polymers512,3736
Non-polymers1,17711
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein DEAD/DEAH box helicase


Mass: 237744.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 str. EDL933 (bacteria)
Gene: Z5898, AU473_27440 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A4P8BDA5
#2: DNA chain DNA (5'-D(P*AP*TP*CP*GP*AP*TP*AP*GP*TP*CP*TP*CP*TP*AP*GP*GP*CP*TP*GP*CP*CP*AP*G)-3')


Mass: 9191.942 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')


Mass: 9249.995 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
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: DruE:ATPgammaS:DNA / Type: COMPLEX / Entity ID: #1, #3, #2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli O157:H7 str. EDL933 (bacteria)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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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 magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 40.57 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2724

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 660861
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21364 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 252.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002633269
ELECTRON MICROSCOPYf_angle_d0.591945407
ELECTRON MICROSCOPYf_chiral_restr0.03874956
ELECTRON MICROSCOPYf_plane_restr0.00345654
ELECTRON MICROSCOPYf_dihedral_angle_d14.23345097

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