9LJF | pdb_00009ljf

Cryo-EM structure of the dGTP bound DRT2-ncRNA complex

• PDB DOI: https://doi.org/10.2210/pdb9LJF/pdb
• EM Map EMD-63147: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN/RNA/DNA
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-01-15 Released: 2026-07-15 
• Deposition Author(s): Zhang, J.T., Qing, H., Xia, Y.S., Jia, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dual sensing activates antiviral reverse transcriptase for membrane targeting

Jia, N., Zhang, J.T., Xia, Y.S., Qi, H., Song, X.Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 141.83 kDa 
• Atom Count: 6,697 
• Modeled Residue Count: 568 
• Deposited Residue Count: 710 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-dependent DNA polymerase	A	425	Klebsiella pneumoniae	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (280-MER)	B	280	Klebsiella pneumoniae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*TP*AP*T)-3')	C	5	Klebsiella pneumoniae

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT (Subject of Investigation/LOI)	F [auth B]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
MG (Subject of Investigation/LOI)	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-15 
Deposition Author(s): Zhang, J.T., Qing, H., Xia, Y.S., Jia, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-07-15
  Type: Initial release