24NC | pdb_000024nc

DRT4 homohexamer with dGTP, RNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 24NC

This is version 1.2 of the entry. See complete history

Literature

DNA polymerization activates RNA cleavage of a reverse transcriptase-like antiviral enzyme.

Rong, X.Xiao, J.Zhao, X.Yan, Y.Li, J.Chen, Y.Fan, Y.Liu, Z.Cao, Y.Chen, F.Cheng, R.Wang, X.Wang, L.Zhu, B.

(2026) Science : eaef3178-eaef3178

  • DOI: https://doi.org/10.1126/science.aef3178
  • Primary Citation Related Structures: 
    21OU, 21RO, 21RP, 21RS, 21WO, 24NA, 24NB, 24NC, 24ND

  • PubMed Abstract: 

    Defense-associated reverse transcriptases (DRTs) transcribe noncoding RNAs (ncRNAs) for antiviral defense, but the mechanisms of ncRNA-independent DRTs remain unclear. In this work, we show that a single DRT4 mediates RNA-targeting antiphage defense by integrating DNA polymerase, exonuclease, and RNA endonuclease activities. First, through an equilibrium between its DNA polymerase and exonuclease activities, DRT4 senses phage infection, as elevated dNTP levels shift the equilibrium toward polymerase activity, thereby promoting protein-primed single-stranded DNA (ssDNA) synthesis. Second, ssDNA of sufficient length, phage DNA-binding proteins, and deoxyguanosine triphosphate collectively activate an unusual RNA endonuclease activity of DRT4, excising 3'-guanosine monophosphate from both phage and host RNA to terminate infection. These findings reveal a distinctive immune strategy combining nucleic acid synthesis and degradation, expanding the functional landscape of DRTs for new DNA- and RNA-processing technologies.


  • Organizational Affiliation
    • Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 384.22 kDa 
  • Atom Count: 26,046 
  • Modeled Residue Count: 3,120 
  • Deposited Residue Count: 3,240 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Reverse transcriptase domain-containing protein
A, B, C, D, E
A, B, C, D, E, F
540EnterobacteriaceaeMutation(s): 0 
Gene Names: BZ227_14395
UniProt
Find proteins for A0A628R156 (Salmonella muenchen)
Explore A0A628R156 
Go to UniProtKB:  A0A628R156
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A628R156
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGT
(Subject of Investigation/LOI)

Query on DGT



Download:Ideal Coordinates CCD File
AA [auth E]
FA [auth F]
G [auth A]
L [auth B]
Q [auth C]
AA [auth E],
FA [auth F],
G [auth A],
L [auth B],
Q [auth C],
V [auth D]
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
DGP

Query on DGP



Download:Ideal Coordinates CCD File
DA [auth E]
IA [auth F]
J [auth A]
O [auth B]
T [auth C]
DA [auth E],
IA [auth F],
J [auth A],
O [auth B],
T [auth C],
Y [auth D]
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
GMP
(Subject of Investigation/LOI)

Query on GMP



Download:Ideal Coordinates CCD File
EA [auth E]
JA [auth F]
K [auth A]
P [auth B]
U [auth C]
EA [auth E],
JA [auth F],
K [auth A],
P [auth B],
U [auth C],
Z [auth D]
GUANOSINE
C10 H13 N5 O5
NYHBQMYGNKIUIF-UUOKFMHZSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
BA [auth E]
CA [auth E]
GA [auth F]
H [auth A]
HA [auth F]
BA [auth E],
CA [auth E],
GA [auth F],
H [auth A],
HA [auth F],
I [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
W [auth D],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

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: 2026-05-27
    Type: Initial release
  • Version 1.1: 2026-06-03
    Changes: Data collection, Database references
  • Version 1.2: 2026-06-10
    Changes: Data collection, Database references