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- PDB-9tu7: CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - m... -

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Basic information

Entry
Database: PDB / ID: 9tu7
TitleCryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - monomer
Components
  • DEAD/DEAH box helicase
  • DNA (30-MER)
  • DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-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: 2.9 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: To Be Published
Title: CryoEM structure of DruE:ATPgammaS:DNA from Druantia type III - monomer
Authors: Grass, L.M. / Himpich, S. / Hilal, T. / Loll, B. / Wahl, M.C.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (30-MER)
Y: DEAD/DEAH box helicase
G: DNA (5'-D(P*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,0379
Polymers256,1873
Non-polymers8506
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: DNA chain DNA (30-MER)


Mass: 9191.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein DEAD/DEAH box helicase


Mass: 237744.781 Da / Num. of mol.: 1
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
#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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: 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
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 / 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
1cryoSPARC2.15particle selection
2EPU3.8image acquisition
4cryoSPARC2.15CTF correction
9cryoSPARC2.15initial Euler assignment
10cryoSPARC2.15final Euler assignment
11cryoSPARC2.15classification
12cryoSPARC2.153D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 660861
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232203 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 127.95 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004117319
ELECTRON MICROSCOPYf_angle_d0.549323664
ELECTRON MICROSCOPYf_chiral_restr0.03872574
ELECTRON MICROSCOPYf_plane_restr0.00362934
ELECTRON MICROSCOPYf_dihedral_angle_d15.09252701

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