9P4J | pdb_00009p4j

The structure of Retron Eco8 in Apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 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

Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity.

Yu, C.Wang, C.Forman, T.Xie, J.Major, S.Fang, M.X.Voyer, J.E.Pogliano, J.Fu, T.M.

(2025) Mol Cell 85: 4243

  • DOI: https://doi.org/10.1016/j.molcel.2025.10.007
  • Primary Citation of Related Structures:  
    9P4J, 9P4K

  • PubMed Abstract: 

    Retrons are antiphage defense systems that synthesize multicopy single-stranded DNA (msDNA) and are being adapted for genome engineering. The Escherichia coli retron Eco8 system comprises a reverse transcriptase (RT), an msDNA, and an overcoming lysogenization defect (OLD)-family nuclease (Eco8-OLD), reminiscent of Gabija. Here, we present the cryo-electron microscopy structure of the Eco8 supramolecular complex, a symmetric 4:4:4 assembly of RT, Eco8-OLD, and msDNA (a hybrid of msrRNA and msdDNA). The msDNA anchors RT and Eco8-OLD into a compact architecture that traps Eco8-OLD in an autoinhibited conformation. Upon phage infection, phage single-stranded DNA-binding proteins (SSBs) bind msdDNA, inducing conformational rearrangements that relieve Eco8-OLD autoinhibition and activate its non-specific DNA nuclease activity. This structural transition enables Eco8 to mount a robust antiphage response by restricting phage genome amplification. Our findings reveal a previously unrecognized mechanism of retron activation and highlight the central role of msDNA as a molecular switch in controlling retron-mediated antiphage defense.


  • Organizational Affiliation
    • Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA; RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retron Eco8 OLD nuclease
A, B, C, D
750Escherichia coliMutation(s): 0 
Gene Names: oldERS139198_01420Ga0119705_103344
EC: 3.1
UniProt
Find proteins for P0DV58 (Escherichia coli)
Explore P0DV58 
Go to UniProtKB:  P0DV58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DV58
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Retron Eco8 reverse transcriptase
E, F, G, H
381Escherichia coliMutation(s): 0 
Gene Names: retERS139198_01421Ga0119705_103345
EC: 2.7.7.49
UniProt
Find proteins for P0DV59 (Escherichia coli)
Explore P0DV59 
Go to UniProtKB:  P0DV59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DV59
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
msrRNAI,
K [auth J],
L [auth K],
M [auth L]
81Escherichia coli
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
msdDNAJ [auth M],
N,
O,
P
75Escherichia coli
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:
RECONSTRUCTIONcryoSPARC

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references