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- PDB-9vhl: cryoEM structure of retron-Eco7 complex (form II) -

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Basic information

Entry
Database: PDB / ID: 9vhl
TitlecryoEM structure of retron-Eco7 complex (form II)
Components
  • Retron Ec78 probable ATPase
  • Retron Ec78 putative HNH endonuclease
  • Retron Ec78 reverse transcriptase
  • msdDNA
  • msrRNA
KeywordsDNA BINDING PROTEIN/RNA/DNA / retron-Eco7 / toxin-antitoxin / DNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / endonuclease activity / defense response to virus / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. ...: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / RNA / RNA (> 10) / Retron Ec78 probable ATPase / Retron Ec78 putative HNH endonuclease / Retron Ec78 reverse transcriptase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsDai, Z.K. / Wang, Y.J. / Guan, Z.Y. / Zou, T.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Phage nuclease-mediated defense activation of the bacterial Retron-Eco7 toxin-antitoxin system.
Authors: Zhikang Dai / Chang Liu / Yanjing Wang / Xueting Chen / Xiaofang Fu / Kaiyue Yang / Rui Zhu / Xianyue Jia / Yanke Chen / Pan Tao / Zeyuan Guan / Tingting Zou /
Abstract: Retrons are bacterial antiphage defense systems comprising a reverse transcriptase (RT), a non-coding RNA (ncRNA), and cognate effector proteins. The RT synthesizes multicopy single-stranded DNA ...Retrons are bacterial antiphage defense systems comprising a reverse transcriptase (RT), a non-coding RNA (ncRNA), and cognate effector proteins. The RT synthesizes multicopy single-stranded DNA (msDNA) from the ncRNA template to detect phage invasion. This study focuses on Retron-Eco7, which integrates retron-based sensing with the effector module of Septu-a characterized antiphage system in which the PtuAB complex mediates nuclease-dependent defense. However, the activation mechanism of this hybrid system remains unclear. Here, we determined cryo-electron microscopy structures of the RT-msDNA-PtuAB quaternary complex and the PtuAB binary complex in Retron-Eco7. Structural analyses reveal that the DNA stem-loop of msDNA extensively interacts with PtuA subunits via electrostatic interactions. We establish Retron-Eco7 as a novel toxin-antitoxin system, in which RT-msDNA acts as the antitoxin, directly binding and neutralizing the PtuAB toxin. Furthermore, we identified a phage-encoded flap endonuclease as a trigger for Retron-Eco7 activation, which cleaves msDNA to release the PtuAB toxin. Our findings demonstrate the diversity in bacterial retron defense systems and uncover a novel activation mechanism of the Septu-derived retron toxin-antitoxin system.
History
DepositionJun 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 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: Retron Ec78 reverse transcriptase
B: Retron Ec78 probable ATPase
C: Retron Ec78 probable ATPase
D: Retron Ec78 probable ATPase
E: Retron Ec78 probable ATPase
F: Retron Ec78 putative HNH endonuclease
G: msdDNA
H: msrRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,54112
Polymers353,9968
Non-polymers1,5464
Water00
1


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

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Components

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Protein , 3 types, 6 molecules ABCDEF

#1: Protein Retron Ec78 reverse transcriptase / RT


Mass: 35629.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ret, Ga0100609_101822 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q46666, RNA-directed DNA polymerase
#2: Protein
Retron Ec78 probable ATPase


Mass: 62466.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ga0100609_101823 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DV91
#3: Protein Retron Ec78 putative HNH endonuclease / TIGR02646 family protein


Mass: 24816.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ga0100609_101824 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DV92

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DNA chain / RNA chain , 2 types, 2 molecules GH

#4: DNA chain msdDNA


Mass: 22869.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 437205
#5: RNA chain msrRNA


Mass: 20813.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 437205

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: retron-Eco7 complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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: 1600 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: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291980 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å

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