9P4K | pdb_00009p4k

The structure of Retron Eco8-SSB complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9P4K

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 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.

Macromolecule Content 

  • Total Structure Weight: 722.8 kDa 
  • Atom Count: 44,547 
  • Modeled Residue Count: 4,820 
  • Deposited Residue Count: 5,148 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
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
Find similar proteins by:|  3D Structure
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
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
msdDNAI [auth O],
J [auth P],
L [auth M],
P [auth N]
75Escherichia coli
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
msrRNAK [auth I],
M [auth J],
N [auth K],
O [auth L]
81Escherichia coli
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 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