9E8Z | pdb_00009e8z

4-component structure of retron Ec83

  • Classification: ANTIVIRAL PROTEIN
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2024-11-06 Released: 2025-07-02 
  • Deposition Author(s): Rish, A.D., Wang, C., Fu, T.M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Disassembly activates Retron-Septu for antiphage defense.

Wang, C.Rish, A.D.Armbruster, E.G.Xie, J.Loveland, A.B.Shen, Z.Gu, B.Korostelev, A.A.Pogliano, J.Fu, T.M.

(2025) Science 389: eadv3344-eadv3344

  • DOI: https://doi.org/10.1126/science.adv3344
  • Primary Citation of Related Structures:  
    9E8Z, 9E90, 9E91, 9O4A

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Pathology, UMass Chan Medical School, Worcester, MA, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retron Ec83 probable ATPaseA [auth C],
F [auth A],
H [auth D],
I [auth F]
542Escherichia coliMutation(s): 0 
Gene Names: Ga0124318_11282
UniProt
Find proteins for Q47527 (Escherichia coli)
Explore Q47527 
Go to UniProtKB:  Q47527
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UniProt GroupQ47527
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Retron Ec83 putative HNH endonucleaseB [auth E],
G [auth B]
260Escherichia coliMutation(s): 0 
Gene Names: Ga0124318_11283
UniProt
Find proteins for P0DV93 (Escherichia coli)
Explore P0DV93 
Go to UniProtKB:  P0DV93
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UniProt GroupP0DV93
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Retron Ec83 reverse transcriptaseC [auth H]312Escherichia coliMutation(s): 0 
Gene Names: retGa0124318_11281
EC: 2.7.7.49
UniProt
Find proteins for Q47526 (Escherichia coli)
Explore Q47526 
Go to UniProtKB:  Q47526
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UniProt GroupQ47526
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (79-MER), msDNAD [auth I]83Escherichia coli
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (38-MER)E [auth J]38Escherichia coli
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGR128399
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1F31AI181575-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references