9IOA | pdb_00009ioa

Cryo-EM structure of the tetrameric DRT9-ncRNA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Resolution: 2.59 Å
  • Resolution: 2.59 Å
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9IOA

This is version 1.1 of the entry. See complete history

Literature

Bacterial reverse transcriptase synthesizes long poly(A)-rich cDNA for antiphage defense.

Song, X.Y.Xia, Y.Zhang, J.T.Liu, Y.J.Qi, H.Wei, X.Y.Hu, H.Xia, Y.Liu, X.Ma, Y.F.Jia, N.

(2025) Science 388: eads4639-eads4639

  • DOI: https://doi.org/10.1126/science.ads4639
  • Primary Citation Related Structures: 
    9IOA, 9IOB

  • PubMed Abstract: 

    Prokaryotic defense-associated reverse transcriptases (DRTs) were recently identified with antiviral functions; however, their functional mechanisms remain largely unexplored. Here we show that DRT9 forms a hexameric complex with its upstream non-coding RNA (ncRNA) to mediate antiphage defense by inducing cell growth arrest via abortive infection. Upon phage infection, the phage-encoded ribonucleotide reductase NrdAB complex elevates intracellular dATP levels, activating DRT9 to synthesize long, poly-A-rich single-stranded cDNA, which likely sequesters the essential phage SSB protein and disrupts phage propagation. We further determined the cryo-electron microscopy structure of the DRT9-ncRNA hexamer complex, providing mechanistic insights into its cDNA synthesis. These findings highlight the diversity of RT-based antiviral defense mechanisms, expand our understanding of RT biological functions, and provide a structural basis for developing DRT9-based biotechnological tools.


  • Organizational Affiliation
    • Department of Biochemistry, SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, China.

Macromolecule Content 

  • Total Structure Weight: 460.45 kDa 
  • Atom Count: 31,104 
  • Modeled Residue Count: 2,660 
  • Deposited Residue Count: 2,704 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-dependent DNA polymeraseD [auth A],
F [auth C],
G [auth E],
H [auth G]
499Escherichia coliMutation(s): 0 
Gene Names: GQA06_05700
UniProt
Find proteins for A0A6D0I497 (Escherichia coli)
Explore A0A6D0I497 
Go to UniProtKB:  A0A6D0I497
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6D0I497
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (177-MER)A [auth D],
B [auth F],
C [auth H],
E [auth B]
177Escherichia coli
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Resolution: 2.59 Å
  • Resolution: 2.59 Å
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection, Database references