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- PDB-9vdp: Cryo-EM structure of the hexameric DRT4 -

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Basic information

Entry
Database: PDB / ID: 9vdp
TitleCryo-EM structure of the hexameric DRT4
Components
  • DNA (5'-D(P*CP*CP*CP*AP*A)-3')
  • Reverse transcriptase domain-containing protein
KeywordsDNA BINDING PROTEIN/DNA / UG15 / DRT4 / Reverse transcriptases / UG/Abi system / DNA BINDING PROTEIN-DNA complex
Function / homologyReverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA / Reverse transcriptase domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsWang, Y. / Deng, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Anti-phage defense mechanism involving phage-encoded DNA binding protein and bacterial reverse transcriptase DRT4.
Authors: Yong Wang / Hao Wu / Jinyue Li / Qiyin An / Zhenhua Tian / Zengqin Deng /
Abstract: Prokaryotic defense-associated reverse transcriptase (DRT) systems confer host resistance to viral infection through DNA synthesis; however, the molecular mechanisms underlying their function remain ...Prokaryotic defense-associated reverse transcriptase (DRT) systems confer host resistance to viral infection through DNA synthesis; however, the molecular mechanisms underlying their function remain poorly understood. Here, we demonstrate that DRT4, a single-gene anti-phage defense system, synthesizes single-stranded DNA (ssDNA) products of random sequences in a template-independent manner. High-resolution cryo-EM structures of DRT4 in multiple functional states elucidate its oligomeric architecture, catalytic metal ion coordination, and substrate/DNA product binding, offering mechanistic insights into its promiscuous polymerization activity. Structural and biochemical analyses further identify a conserved tyrosine residue that acts as the priming site for the initiation of DNA synthesis. Upon phage infection, a phage-encoded DNA-binding protein, ORF55, protects the 3' end of the DRT4-synthesized ssDNA from host exonuclease degradation, likely resulting in toxic ssDNA accumulation that leads to cell death. Remarkably, ORF55 also activates DRT6, a structural homolog of DRT4, suggesting a conserved activation mechanism among related DRT systems. These findings provide structural and mechanistic insights into DRT4-mediated antiviral defense, establishing a distinct paradigm for antiviral reverse transcriptase in bacterial immunity.
History
DepositionJun 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jan 21, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jan 21, 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
A: Reverse transcriptase domain-containing protein
I: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
B: Reverse transcriptase domain-containing protein
C: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
D: Reverse transcriptase domain-containing protein
E: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
F: Reverse transcriptase domain-containing protein
G: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
H: Reverse transcriptase domain-containing protein
J: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
K: Reverse transcriptase domain-containing protein
L: DNA (5'-D(P*CP*CP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)392,16012
Polymers392,16012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Reverse transcriptase domain-containing protein


Mass: 63911.047 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BZ227_14395 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A628R156
#2: DNA chain
DNA (5'-D(P*CP*CP*CP*AP*A)-3')


Mass: 1449.002 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
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: DRT4-DNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 306468 / Symmetry type: POINT
RefinementHighest resolution: 2.27 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425662
ELECTRON MICROSCOPYf_angle_d0.70434860
ELECTRON MICROSCOPYf_dihedral_angle_d14.823606
ELECTRON MICROSCOPYf_chiral_restr0.0483768
ELECTRON MICROSCOPYf_plane_restr0.0064356

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