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- PDB-9e8z: 4-component structure of retron Ec83 -

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Basic information

Entry
Database: PDB / ID: 9e8z
Title4-component structure of retron Ec83
Components
  • DNA (79-MER), msDNA
  • RNA (38-MER)
  • Retron Ec83 probable ATPase
  • Retron Ec83 putative HNH endonuclease
  • Retron Ec83 reverse transcriptase
KeywordsANTIVIRAL PROTEIN / ATPase / HNH-Endonuclease / Retron / msDNA
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / RNA-directed DNA polymerase activity / RNA-directed DNA polymerase / 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 / RNA-directed DNA polymerase (reverse transcriptase), msDNA / AAA domain, group 15 / AAA ATPase domain / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / ATPases associated with a variety of cellular activities ...: / Retron Ec78 putative HNH endonuclease-like / RNA-directed DNA polymerase (reverse transcriptase), msDNA / AAA domain, group 15 / AAA ATPase domain / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / DNA / DNA (> 10) / RNA / RNA (> 10) / Retron Ec83 putative HNH endonuclease / Retron Ec83 reverse transcriptase / Retron Ec83 probable ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsRish, A.D. / Wang, C. / Fu, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GR128399 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31AI181575-01 United States
CitationJournal: Science / Year: 2025
Title: Disassembly activates Retron-Septu for antiphage defense.
Authors: Chen Wang / Anthony D Rish / Emily G Armbruster / Jiale Xie / Anna B Loveland / Zhangfei Shen / Bradley Gu / Andrei A Korostelev / Joe Pogliano / Tian-Min Fu /
Abstract: Retrons are antiphage defense systems that produce multicopy single-stranded DNA (msDNA) and hold promises for genome engineering. However, the mechanisms of defense remain unclear. The Retron-Septu ...Retrons are antiphage defense systems that produce multicopy single-stranded DNA (msDNA) and hold promises for genome engineering. However, the mechanisms of defense remain unclear. The Retron-Septu system uniquely integrates retron and Septu antiphage defenses. Cryo-electron microscopy structures reveal asymmetric nucleoprotein complexes comprising a reverse transcriptase (RT), msDNA (a hybrid of msdDNA and msrRNA), and two PtuAB copies. msdDNA and msrRNA are essential for assembling this complex, with msrRNA adopting a conserved lariat-like structure that regulates reverse transcription. Notably, the assembled Retron-Septu complex is inactive, with msdDNA occupying the PtuA DNA-binding site. Activation occurs upon disassembly, releasing PtuAB, which degrades single-stranded DNA to restrict phage replication. This "arrest-and-release" mechanism underscores the dynamic regulatory roles of msDNA, advancing our understanding of antiphage defense strategies.
History
DepositionNov 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Retron Ec83 probable ATPase
E: Retron Ec83 putative HNH endonuclease
H: Retron Ec83 reverse transcriptase
I: DNA (79-MER), msDNA
J: RNA (38-MER)
A: Retron Ec83 probable ATPase
B: Retron Ec83 putative HNH endonuclease
D: Retron Ec83 probable ATPase
F: Retron Ec83 probable ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,97913
Polymers380,9949
Non-polymers9854
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

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Protein , 3 types, 7 molecules CADFEBH

#1: Protein
Retron Ec83 probable ATPase


Mass: 61767.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ATPase / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ga0124318_11282 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47527
#2: Protein Retron Ec83 putative HNH endonuclease / TIGR02646 family protein


Mass: 30233.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HNH-endonuclease / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ga0124318_11283 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DV93
#3: Protein Retron Ec83 reverse transcriptase / RT


Mass: 35794.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RT / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ret, Ga0124318_11281 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47526, RNA-directed DNA polymerase

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

#4: DNA chain DNA (79-MER), msDNA


Mass: 25559.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: msDNA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 42499
#5: RNA chain RNA (38-MER)


Mass: 12102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
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: Complete Ec83 retron complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80872 / Symmetry type: POINT
RefinementHighest resolution: 3.47 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325342
ELECTRON MICROSCOPYf_angle_d0.61534876
ELECTRON MICROSCOPYf_dihedral_angle_d18.4364465
ELECTRON MICROSCOPYf_chiral_restr0.0414015
ELECTRON MICROSCOPYf_plane_restr0.0054066

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