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- PDB-21ou: DRT4 homohexamer -

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Basic information

Entry
Database: PDB / ID: 21ou
TitleDRT4 homohexamer
Components
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Reverse transcriptase domain-containing protein
KeywordsRNA BINDING PROTEIN/DNA / DRT4 / reverse transcriptase / terminal transferase / nuclease / RNA BINDING PROTEIN-DNA complex
Function / homologyReverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA / Reverse transcriptase domain-containing protein
Function and homology information
Biological speciesEnterobacteriaceae (enterobacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsXiao, J. / Wang, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2026
Title: DNA polymerization activates RNA cleavage of a reverse transcriptase-like antiviral enzyme.
Authors: Xuejun Rong / Jun Xiao / Xinyuan Zhao / Yan Yan / Jing Li / Yifan Chen / Yihua Fan / Zhichao Liu / Yue Cao / Fan Chen / Rui Cheng / Xionglue Wang / Longfei Wang / Bin Zhu /
Abstract: Defense-associated reverse transcriptases (DRTs) transcribe noncoding RNAs (ncRNAs) for antiviral defense, but the mechanisms of ncRNA-independent DRTs remain unclear. In this work, we show that a ...Defense-associated reverse transcriptases (DRTs) transcribe noncoding RNAs (ncRNAs) for antiviral defense, but the mechanisms of ncRNA-independent DRTs remain unclear. In this work, we show that a single DRT4 mediates RNA-targeting antiphage defense by integrating DNA polymerase, exonuclease, and RNA endonuclease activities. First, through an equilibrium between its DNA polymerase and exonuclease activities, DRT4 senses phage infection, as elevated dNTP levels shift the equilibrium toward polymerase activity, thereby promoting protein-primed single-stranded DNA (ssDNA) synthesis. Second, ssDNA of sufficient length, phage DNA-binding proteins, and deoxyguanosine triphosphate collectively activate an unusual RNA endonuclease activity of DRT4, excising 3'-guanosine monophosphate from both phage and host RNA to terminate infection. These findings reveal a distinctive immune strategy combining nucleic acid synthesis and degradation, expanding the functional landscape of DRTs for new DNA- and RNA-processing technologies.
History
DepositionDec 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Jun 3, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 2.0Jun 3, 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
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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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
B: Reverse transcriptase domain-containing protein
C: Reverse transcriptase domain-containing protein
D: Reverse transcriptase domain-containing protein
E: Reverse transcriptase domain-containing protein
F: Reverse transcriptase domain-containing protein
G: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
H: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
I: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
J: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
K: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
L: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)391,87012
Polymers391,87012
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
Reverse transcriptase domain-containing protein


Mass: 62850.957 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Enterobacteriaceae' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A628R156.
Source: (gene. exp.) Enterobacteriaceae (enterobacteria) / Gene: BZ227_14395 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A628R156
#2: DNA chain
DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2460.697 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteriaceae (enterobacteria) / 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 homohexamer / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Enterobacteriaceae (enterobacteria)
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

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: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217690 / Symmetry type: POINT
RefinementHighest resolution: 2.34 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00227078
ELECTRON MICROSCOPYf_angle_d0.38436858
ELECTRON MICROSCOPYf_dihedral_angle_d14.3924062
ELECTRON MICROSCOPYf_chiral_restr0.0363972
ELECTRON MICROSCOPYf_plane_restr0.0034554

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