9C0I | pdb_00009c0i

Structure of the DRT2 reverse transcriptase in complex with its non-coding RNA

• PDB DOI: https://doi.org/10.2210/pdb9C0I/pdb
• EM Map EMD-45085: EMDB EMDataResource
• NAKB: 9C0I

• Classification: TRANSFERASE/DNA/RNA
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-25 Released: 2024-09-04 
• Deposition Author(s): Wilkinson, M.E., Zhang, F.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.91 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA.

Wilkinson, M.E., Li, D., Gao, A., Macrae, R.K., Zhang, F.

(2024) Science 386: eadq3977-eadq3977

• PubMed: 39208082 
• DOI: https://doi.org/10.1126/science.adq3977
• Primary Citation Related Structures: 
  9C0I, 9C0J


• PubMed Abstract: 
  

  Reverse transcription has frequently been co-opted for cellular functions and in prokaryotes is associated with protection against viral infection, but the underlying mechanisms of defense are generally unknown. Here, we show that in the DRT2 defense system the reverse transcriptase binds a neighboring pseudoknotted noncoding RNA. Upon bacteriophage infection, a template region of this RNA is reverse transcribed into an array of tandem repeats that reconstitute a promoter and open reading frame, allowing expression of a toxic repetitive protein and an abortive infection response. Biochemical reconstitution of this activity and cryogenic electron microscopy provide a molecular basis for repeat synthesis. Gene synthesis from a noncoding RNA is a new mode of genetic regulation in prokaryotes.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 142.32 kDa 
• Atom Count: 7,676 
• Modeled Residue Count: 622 
• Deposited Residue Count: 713 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/maturase family protein	A	425	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: QIG75_19540

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA primer	B [auth P]	5	Klebsiella pneumoniae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DRT2 ncRNA	C [auth R]	283	Klebsiella pneumoniae

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	E [auth R]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.91 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	4.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Wilkinson, M.E., Zhang, F.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-09-11
  Changes: Data collection, Database references
• Version 1.2: 2024-09-18
  Changes: Data collection
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2025-05-21
  Changes: Data collection