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- PDB-9o4a: Ec83 Retron PtuAB mutant complex -

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Basic information

Entry
Database: PDB / ID: 9o4a
TitleEc83 Retron PtuAB mutant complex
Components
  • Retron Ec83 probable ATPase
  • Retron Ec83 putative HNH endonuclease
KeywordsIMMUNE SYSTEM / retron / PtuA / PtuB / ATPase / HNH nuclease
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / double-strand break repair / endonuclease activity / defense response to virus / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / Retron Ec78 putative HNH endonuclease-like / AAA domain, group 15 / AAA ATPase domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Retron Ec83 putative HNH endonuclease / Retron Ec83 probable ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang, C. / Rish, A. / Fu, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionApr 8, 2025Deposition 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
A: Retron Ec83 probable ATPase
B: Retron Ec83 probable ATPase
C: Retron Ec83 putative HNH endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5786
Polymers153,4983
Non-polymers1,0803
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 Retron Ec83 probable ATPase


Mass: 61665.863 Da / Num. of mol.: 2 / Mutation: D399A, E400A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ga0124318_11282 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47527
#2: Protein Retron Ec83 putative HNH endonuclease / TIGR02646 family protein


Mass: 30166.254 Da / Num. of mol.: 1 / Mutation: H71A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ga0124318_11283 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DV93
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: Ec83 PtuAB complex / Type: COMPLEX / Entity ID: #1-#2 / 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

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 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 965923 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038977
ELECTRON MICROSCOPYf_angle_d0.68212159
ELECTRON MICROSCOPYf_dihedral_angle_d6.2631207
ELECTRON MICROSCOPYf_chiral_restr0.0451367
ELECTRON MICROSCOPYf_plane_restr0.0051555

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