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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: To Be Published
Title: Semirandom DNA adducts regulate a filamentous defense-associated reverse transcriptase
Authors: Neville, N. / Johnson, N.V. / Escobar, E.E. / Chiang, C.H. / Nreca, A. / Johnson, S.R. / Dai, N. / Hanneman, A. / Correa Jr., I.R. / McLellan, J.S. / Trachman III., R.J.
History
DepositionSep 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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