23OR | pdb_000023or

Cryo-EM structure of the Retron-Eco8-SSB complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Mechanistic insights into activation of bacterial Retron-Eco8 immunity by phage protein SSB.

Ji, C.G.Li, Z.Wei, X.Y.Li, Y.Zhang, J.T.Liu, X.Jia, N.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-74106-9
  • Primary Citation Related Structures: 
    23OR, 9LBQ, 9WN8

  • PubMed Abstract: 

    The Retron-Eco8 system, comprising a reverse transcriptase (RT), a non-coding RNA (ncRNA), and an OLD-family nuclease effector, protects bacteria from phage infection via abortive infection upon sensing a phage single-stranded DNA-binding protein (SSB). However, the molecular basis of this immunity remained unclear. Here, we report cryo-electron microscopy (cryo-EM) structures of Retron-Eco8 in inactive and activated states, revealing mechanisms of phage-triggered activation and effector function. Retron-Eco8 assembles into a tetrameric complex in which each protomer contains an RT, msrRNA-msdDNA duplex, and effector in an autoinhibited conformation. Upon phage infection, phage SSB binds msdDNA, relieving autoinhibition and activating the nuclease effector to degrade both phage and host DNA, triggering cell death to block phage propagation. Host SSB fails to activate the system, while DNA binding and oligomerization of phage SSB are essential for this activation, highlighting its specificity. These findings elucidate the molecular mechanism of Retron-Eco8-mediated immunity, facilitating retron-based biotechnological applications.


  • Organizational Affiliation
    • Department of Critical Care Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Department of Biochemistry, SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, China.

Macromolecule Content 

  • Total Structure Weight: 721.74 kDa 
  • Atom Count: 42,224 
  • Modeled Residue Count: 4,538 
  • Deposited Residue Count: 5,128 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retron Eco8 reverse transcriptase
A, E, I, M
374Escherichia 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 proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Retron Eco8 OLD nuclease
B, F, J, N
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 nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (83-MER)
C, G, K, O
83Escherichia coli
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (75-MER)
D, H, L, P
75Escherichia coli
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-08
    Type: Initial release