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- PDB-9yfd: Defense-associated reverse transcriptase 1 (DRT1) filament -

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Basic information

Entry
Database: PDB / ID: 9yfd
TitleDefense-associated reverse transcriptase 1 (DRT1) filament
ComponentsDefense-associated reverse transcriptase 1
KeywordsANTIVIRAL PROTEIN / Anti-phage defense / DNA synthesis / Nitrilase domain / RT domain / filament
Function / homology2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJohnson, N.V. / McLellan, J.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Semirandom DNA adducts regulate a filamentous defense-associated reverse transcriptase.
Authors: Nolan Neville / Nicole V Johnson / Edwin E Escobar / Chang-Hwa Chiang / Albana Nreca / Sean R Johnson / Nan Dai / Andy Hanneman / Ivan R Corrêa / Jason S McLellan / Robert J Trachman /
Abstract: Retrons and several defense-associated reverse transcriptases (DRTs) synthesize non-genomic DNA for bacteriophage immunity. In some instances, this non-genomic DNA is of undefined, semirandom ...Retrons and several defense-associated reverse transcriptases (DRTs) synthesize non-genomic DNA for bacteriophage immunity. In some instances, this non-genomic DNA is of undefined, semirandom sequence. How undefined DNA sequences impart antiphage defense is not known. Herewe report the cryo-EM structure and functional characterization of the DRT1 antiphage defense system. We show that DRT1 performs template-free, protein-primed DNA synthesis to generate semirandom DNA adducts. DNA synthesis activates the nitrilase domain of DRT1, while DNA adducts drive the assembly of quiescent DRT1 filaments. Filamentous DRT1 is composed of domain-swapped C termini that are entwined, forming pseudoknots between tetrameric stacks. This configuration occludes conserved active-site residues, resulting in a dormant state. Bacteriophage escape mutants identify a T4 single-stranded DNA helicase required for DRT1 activity. Functionally, DRT1 resembles a minimal retron where a single gene produces a reverse transcriptase, effector and non-genomic antitoxin DNA.
History
DepositionSep 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defense-associated reverse transcriptase 1
B: Defense-associated reverse transcriptase 1
C: Defense-associated reverse transcriptase 1
D: Defense-associated reverse transcriptase 1
E: Defense-associated reverse transcriptase 1
F: Defense-associated reverse transcriptase 1
G: Defense-associated reverse transcriptase 1
H: Defense-associated reverse transcriptase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,136,73432
Polymers1,132,4168
Non-polymers4,31824
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
Defense-associated reverse transcriptase 1


Mass: 141551.984 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: DRT1 reacted with dNTPs / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 565 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 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 defocus max: 2400 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1SerialEMparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140634 / Symmetry type: POINT

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