9O4A | pdb_00009o4a

Ec83 Retron PtuAB mutant complex

• PDB DOI: https://doi.org/10.2210/pdb9O4A/pdb
• EM Map EMD-70091: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-04-08 Released: 2025-07-02 
• Deposition Author(s): Wang, C., Rish, A., Fu, T.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 40504952 
• 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.

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Organizational Affiliation: 
• Department of Pathology, UMass Chan Medical School, Worcester, MA, USA.
RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.
Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA.
Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
School of Biological Sciences, University of California, San Diego, San Diego, CA, USA.
Coffman high school, Dublin, OH, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 154.58 kDa 
• Atom Count: 8,804 
• Modeled Residue Count: 1,116 
• Deposited Residue Count: 1,344 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retron Ec83 probable ATPase	A, B	542	Escherichia coli	Mutation(s): 2  Gene Names: Ga0124318_11282
UniProt
Find proteins for Q47527 (Escherichia coli) Explore Q47527  Go to UniProtKB:  Q47527

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retron Ec83 putative HNH endonuclease	C	260	Escherichia coli	Mutation(s): 1  Gene Names: Ga0124318_11283
UniProt
Find proteins for P0DV93 (Escherichia coli) Explore P0DV93  Go to UniProtKB:  P0DV93

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	D [auth A], E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)	F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Wang, C., Rish, A., Fu, T.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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