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- PDB-9z6y: Structure of the elongating EcDRT3 reverse transcriptase in compl... -

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Basic information

Entry
Database: PDB / ID: 9z6y
TitleStructure of the elongating EcDRT3 reverse transcriptase in complex with its non-coding RNA
Components
  • Drt3a reverse transcriptase protein
  • Drt3b reverse transcriptase protein
  • cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
  • cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
  • non-coding RNA
KeywordsIMMUNE SYSTEM / DRT3-ncRNA complex / reverse transcriptase / Anti-phage complex
Function / homologyPYROPHOSPHATE 2- / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsDeng, P. / Gao, A.
Funding support United States, 1items
OrganizationGrant numberCountry
The G. Harold and Leila Y. Mathers FoundationMF-2303-04116 United States
CitationJournal: Science / Year: 2026
Title: Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase.
Authors: Pujuan Deng / Hyunbin Lee / Carlo Armijo / Haoqing Wang / Alex Gao /
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 ...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.
History
DepositionNov 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Drt3a reverse transcriptase protein
B: Drt3a reverse transcriptase protein
C: Drt3a reverse transcriptase protein
D: Drt3a reverse transcriptase protein
E: Drt3a reverse transcriptase protein
F: Drt3a reverse transcriptase protein
H: Drt3b reverse transcriptase protein
I: Drt3b reverse transcriptase protein
J: Drt3b reverse transcriptase protein
K: Drt3b reverse transcriptase protein
L: Drt3b reverse transcriptase protein
M: Drt3b reverse transcriptase protein
R: non-coding RNA
S: non-coding RNA
T: non-coding RNA
U: non-coding RNA
V: non-coding RNA
W: non-coding RNA
X: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
Y: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
Z: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
a: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
b: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
c: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
d: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
e: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
f: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
g: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
h: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
i: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,091,76354
Polymers1,090,26930
Non-polymers1,49324
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 12 molecules ABCDEFHIJKLM

#1: Protein
Drt3a reverse transcriptase protein


Mass: 50345.750 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein
Drt3b reverse transcriptase protein


Mass: 76426.602 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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RNA chain , 1 types, 6 molecules RSTUVW

#3: RNA chain
non-coding RNA


Mass: 44236.227 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1842461545

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DNA chain , 2 types, 12 molecules XZbdfhYacegi

#4: DNA chain
cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')


Mass: 5326.424 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#5: DNA chain
cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')


Mass: 5376.540 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 30 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2O7P2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hexameric complex of DRT3-ncRNA / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239792 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model

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