9Z6Z | pdb_00009z6z

Structure of the resting EcDRT3 reverse transcriptase in complex with its non-coding RNA

• PDB DOI: https://doi.org/10.2210/pdb9Z6Z/pdb
• NAKB: 9Z6Z
• EM Map EMD-73865: EMDB EMDataResource

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


• Deposited: 2025-11-14 Released: 2026-04-29 
• Deposition Author(s): Deng, P., Gao, A.
• Funding Organization(s): The G. Harold and Leila Y. Mathers Foundation

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase.

Deng, P., Lee, H., Armijo, C., Wang, H., Gao, A.

(2026) Science : eaed1656-eaed1656

• PubMed: 41990131 
• DOI: https://doi.org/10.1126/science.aed1656
• Primary Citation Related Structures: 
  9Z6Y, 9Z6Z


• PubMed Abstract: 
  

  Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo-electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.

---

Organizational Affiliation: 
• Department of Biochemistry, Stanford University, Stanford, CA, USA.
Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Department of Biology, Stanford University, Stanford, CA, USA.
Sarafan ChEM-H, Stanford University, Stanford, CA, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,079.1 kDa 
• Atom Count: 69,348 
• Modeled Residue Count: 7,110 
• Deposited Residue Count: 7,458 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Drt3a reverse transcriptase protein	A, B, C, D, E, F	426	Escherichia coli	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Drt3b reverse transcriptase protein	G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M]	650	Escherichia coli	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
non-coding RNA	M [auth R], N [auth S], O [auth T], P [auth U], Q [auth V], R [auth W]	138	Escherichia coli

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*TP*GP*T)-3')	AA [auth f], CA [auth h], S [auth X], U [auth Z], W [auth b], Y [auth d]	12	Escherichia coli

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')	BA [auth g], DA [auth i], T [auth Y], V [auth a], X [auth c], Z [auth e]	17	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	EA [auth H], FA [auth I], GA [auth J], HA [auth K], IA [auth L], JA [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M]	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.0
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-29 
Deposition Author(s): Deng, P., Gao, A.

---

Funding Organization	Location	Grant Number
The G. Harold and Leila Y. Mathers Foundation	United States	MF-2303-04116

Revision History  

• Version 1.0: 2026-04-29
  Type: Initial release