9NLX | pdb_00009nlx

Cryo-EM structure of the trimeric SenDRT9 RT-ncRNA complex (GST fusion)

• PDB DOI: https://doi.org/10.2210/pdb9NLX/pdb
• EM Map EMD-49525: EMDB EMDataResource
• NAKB: 9NLX

• Classification: IMMUNE SYSTEM
• Organism(s): Salmonella enterica
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2025-03-03 Released: 2025-05-14 
• Deposition Author(s): Burman, N., Pandey, S., Wiedenheft, B., Sternberg, S.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Protein-primed homopolymer synthesis by an antiviral reverse transcriptase.

Tang, S., Zedaveinyte, R., Burman, N., Pandey, S., Ramirez, J.L., Kulber, L.M., Wiegand, T., Wilkinson, R.A., Ma, Y., Zhang, D.J., Lampe, G.D., Berisa, M., Jovanovic, M., Wiedenheft, B., Sternberg, S.H.

(2025) Nature 643: 1352-1362

• PubMed: 40436039 
• DOI: https://doi.org/10.1038/s41586-025-09179-5
• Primary Citation Related Structures: 
  9NLV, 9NLX


• PubMed Abstract: 
  

  Bacteria defend themselves from viral predation using diverse immune systems, many of which target foreign DNA for degradation ¹ . Defence-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this strategy by using DNA synthesis instead ^2,3 . We and others recently showed that DRT2 systems use an RNA template to assemble a de novo gene that encodes the antiviral effector protein Neo ^4,5 . It remains unclear whether similar mechanisms of defence are used by other related DRT families. Here, we show that DRT9 systems defend against phage using DNA homopolymer synthesis. Viral infection triggers polydeoxyadenylate (poly-dA) accumulation in the cell, driving abortive infection and population-level immunity. Cryo-electron microscopy structures reveal how a non-coding RNA serves as both a structural scaffold and reverse transcription template to direct hexameric complex assembly and poly-dA synthesis. Notably, biochemical and functional experiments identify tyrosine residues within the reverse transcriptase itself that probably prime DNA synthesis, leading to the formation of protein-DNA covalent adducts. Synthesis of poly-dA by DRT9 in vivo is regulated by the competing activities of phage-encoded triggers and host-encoded silencers. Collectively, our study identifies a nucleic-acid-driven defence system that expands the paradigm of bacterial immunity and broadens the known functions of reverse transcriptases.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
Department of Biological Sciences, Columbia University, New York, NY, USA.
Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Metabolomics Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA. [e-mail].
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. [e-mail].
Howard Hughes Medical Institute, Columbia University, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 316.68 kDa 
• Atom Count: 20,076 
• Modeled Residue Count: 1,884 
• Deposited Residue Count: 1,938 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-dependent DNA polymerase	B [auth A], C [auth B], D [auth C]	499	Salmonella enterica	Mutation(s): 0  Gene Names: GQA06_05700
UniProt
Find proteins for A0A8F5N3I9 (Salmonella diarizonae) Explore A0A8F5N3I9  Go to UniProtKB:  A0A8F5N3I9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (147-MER)	A [auth G], E [auth H], F [auth I]	147	Salmonella enterica

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Burman, N., Pandey, S., Wiedenheft, B., Sternberg, S.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM134867
National Science Foundation (NSF, United States)	United States	2239685

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-06-04
  Changes: Data collection, Database references
• Version 1.2: 2025-06-11
  Changes: Data collection, Database references
• Version 2.0: 2025-08-13
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Data processing, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary