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- PDB-9trd: Bacterial antiviral defense protein PD-T7-3 (H122A) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9trd
TitleBacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA and a fragment of RNA
Components
  • (RNA) x 2
  • Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
  • single-stranded DNA
KeywordsANTIVIRAL PROTEIN / HEPN domain / nuclease / bacterial antiviral protein / PD-T7-3
Function / homologyDNA / DNA (> 10) / RNA
Function and homology information
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsPuteikiene, R. / Sasnauskas, G.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of LithuaniaS-MIP-22-13Lithuania
CitationJournal: To Be Published
Title: Standalone anti-phage HEPN nuclease PD-T7-3 is activated by ssDNA for tRNA cleavage
Authors: Puteikiene, R. / Vassallo, C.N. / Silanskas, A. / Songailiene, I. / Juozapaitis, J. / Laub, M.T. / Sasnauskas, G.
History
DepositionDec 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 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

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Assembly

Deposited unit
A: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
B: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
C: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
S: single-stranded DNA
D: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
E: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
F: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
T: single-stranded DNA
G: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
H: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
I: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
U: single-stranded DNA
J: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
K: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
L: Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A
V: single-stranded DNA
M: RNA
N: RNA


Theoretical massNumber of molelcules
Total (without water)701,29118
Polymers701,29118
Non-polymers00
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
Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A


Mass: 54571.945 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ECOR30 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: DNA chain
single-stranded DNA


Mass: 10358.687 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA


Mass: 2588.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain RNA


Mass: 2404.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: Bacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA and a fragment of RNA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli) / Strain: ECOR30
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 29 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2582

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPU3.11image acquisition
4cryoSPARCCTF correction
9cryoSPARCinitial Euler assignment
11cryoSPARCclassification
12cryoSPARC4.7.13D reconstruction
13PHENIX1.21.2-5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115980
Details: Number of particles after D2 symmetry expansion. Resolution calculated as the mean resolution value of consensus map and two focus maps.
Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE

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