22EU | pdb_000022eu

Cryo-EM structure of Retron Ec78 complex (trans)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Dual-inhibitory mechanism of the bacterial retron Ec78 antiphage defense system.

Lin, Z.Guo, M.Lu, Z.Zhu, Y.Zhou, F.Zhang, A.Guo, C.Huang, Z.

(2026) Proc Natl Acad Sci U S A 123: e2610082123-e2610082123

  • DOI: https://doi.org/10.1073/pnas.2610082123
  • Primary Citation Related Structures: 
    22ET, 22EU

  • PubMed Abstract: 

    Retrons are prokaryotic defense modules that protect bacteria from phage infection through abortive infection. The retron Ec78 system employs a two-component effector complex PtuAB to execute this defense. Despite recent advances in structural research, the molecular mechanism by which PtuAB effector is regulated remains unknown. Here, we reveal that PtuAB is subject to a dual-inhibitory mechanism mediated by ATP/ADP and the RT-msDNA antitoxin. ATP/ADP binds nucleotide-binding domain (NBD) of PtuAB and induces the assembly of an inactive tetrameric complex, whereas the RT-msDNA stabilizes an inhibited conformation of Ec78 complex and stimulates ATP turnover to prime PtuAB for rapid activation. Structural analyses show that RT-msDNA dissociation and nucleotide release from PtuA induce conformational rearrangements in the NBD of PtuA and a downward displacement of a key β-loop-β motif, driving disassembly of the PtuAB tetramer through an allosteric mechanism and thereby activating its tRNA Tyr cleavage activity. Our findings uncover how nucleotides-specifically ATP and ADP-regulate the activity of this abortive infection system, and establish a dual-inhibition model of retron Ec78 system, expanding the understanding of the regulation mechanism of PtuAB activation in prokaryotic immune systems.


  • Organizational Affiliation
    • Harbin Institute of Technology (HIT) Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, Heilongjiang, China.

Macromolecule Content 

  • Total Structure Weight: 383.38 kDa 
  • Atom Count: 26,167 
  • Modeled Residue Count: 3,055 
  • Deposited Residue Count: 3,084 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retron310Escherichia coliMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PtuA
B, C, D, E
551Escherichia coliMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PtuB
F, G
215Escherichia coliMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (74-MER)H [auth M]74Escherichia coli
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (66-MER)I [auth N]66Escherichia coli
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-29
    Type: Initial release
  • Version 1.1: 2026-08-12
    Changes: Data collection, Database references