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- EMDB-72883: Defense-associated reverse transcriptase 1 (DRT1) filament -

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Basic information

Entry
Database: EMDB / ID: EMD-72883
TitleDefense-associated reverse transcriptase 1 (DRT1) filament
Map data
Sample
  • Complex: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
    • Protein or peptide: Defense-associated reverse transcriptase 1
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsAnti-phage defense / DNA synthesis / Nitrilase domain / RT domain / filament / ANTIVIRAL PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJohnson NV / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Semirandom DNA adducts regulate a filamentous defense-associated reverse transcriptase.
Authors: Nolan Neville / Nicole V Johnson / Edwin E Escobar / Chang-Hwa Chiang / Albana Nreca / Sean R Johnson / Nan Dai / Andy Hanneman / Ivan R Corrêa / Jason S McLellan / Robert J Trachman /
Abstract: Retrons and several defense-associated reverse transcriptases (DRTs) synthesize non-genomic DNA for bacteriophage immunity. In some instances, this non-genomic DNA is of undefined, semirandom ...Retrons and several defense-associated reverse transcriptases (DRTs) synthesize non-genomic DNA for bacteriophage immunity. In some instances, this non-genomic DNA is of undefined, semirandom sequence. How undefined DNA sequences impart antiphage defense is not known. Herewe report the cryo-EM structure and functional characterization of the DRT1 antiphage defense system. We show that DRT1 performs template-free, protein-primed DNA synthesis to generate semirandom DNA adducts. DNA synthesis activates the nitrilase domain of DRT1, while DNA adducts drive the assembly of quiescent DRT1 filaments. Filamentous DRT1 is composed of domain-swapped C termini that are entwined, forming pseudoknots between tetrameric stacks. This configuration occludes conserved active-site residues, resulting in a dormant state. Bacteriophage escape mutants identify a T4 single-stranded DNA helicase required for DRT1 activity. Functionally, DRT1 resembles a minimal retron where a single gene produces a reverse transcriptase, effector and non-genomic antitoxin DNA.
History
DepositionSep 25, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72883.png

Downloads & links

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Map

FileDownload / File: emd_72883.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.07320925 - 1.9622343
Average (Standard dev.)0.006095051 (±0.053148303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_72883_additional_1.map
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Half map: #1

Fileemd_72883_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_72883_half_map_2.map
Projections & Slices
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Sample components

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Entire : DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain

EntireName: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
Components
  • Complex: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
    • Protein or peptide: Defense-associated reverse transcriptase 1
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain

SupramoleculeName: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 565 kDa/nm

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Macromolecule #1: Defense-associated reverse transcriptase 1

MacromoleculeName: Defense-associated reverse transcriptase 1 / type: protein_or_peptide / ID: 1 / Details: DRT1 reacted with dNTPs / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 141.551984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLLNKKYYN LEPNFDYLKD SFILGLAWKK TDRFVRTHNW YADLLALDKC AFDISDEVTS WSSEAVNRNL SKSDIELIPA PKRASWFFN KGKWTTNKDD RKLRPLANIS IKDQSFATAV TMCLADAIET RQKDCSLRNL GYAEHVNKKV VSYGNRLVCD W DNERARFR ...String:
MKLLNKKYYN LEPNFDYLKD SFILGLAWKK TDRFVRTHNW YADLLALDKC AFDISDEVTS WSSEAVNRNL SKSDIELIPA PKRASWFFN KGKWTTNKDD RKLRPLANIS IKDQSFATAV TMCLADAIET RQKDCSLRNL GYAEHVNKKV VSYGNRLVCD W DNERARFR WGGSEYYRKF STDYRNFLQR PVYIGRETVN KISEIDDVYI ISLDLKNFFG SIKISTLLEK LKKISSDHYD HN IINENEF WGLASQILNW EWPEDSLSLL KNLDIEEENV GLPQGLASAG ALANAYLIEF DESLTSNLRT KIDGSQIVLH DYC RYVDDI RLVISGEALT NEEIKKSIHE LVQRILDETL DQDESDNEPY LKINDKKTYI LGLSDIDNGS SLTNRINEIQ NEVG TSSIP ERNGLDNNIP ALQQLLLTEQ DNFLEDADGL FSGFNNDKSI KLESLRRFSA HRLETSLANK SKLISPAERK QFDNE SALI AKKLLKTWLK DPSIMVIFRK AITINPNLDA YKTILEIIFL RIQHNREKCD RYIMLYLLSD IFRSVVDIYR KLSPEC TSD YQKLMSEVTS FAHKLLSCRS VIPNYAYQQA LFYLAVINKP FIASKKSSSD LSKLQHVLIK RHLEPLSSSD GYLFELS AQ ISKDYQANVA FLLSHTNTTE VVDSIVEKFA YRGGEFWNSI WKEFVRTKDK VRINKFRWAI PKNESKPNGS DHYLSSVI S FKENPFKYEH ALLKLGIALV NLLEDTEKNV WQSDGKQYSP HEIKVKLEGH STSWTELWRQ NSIISCSIDK IAQDPRYES PKWLVNCQQA KNDEKKIYWV CSVLRSAALG NVDYTQRNDL KPDRVEYDGI HSQFYKRRMG MLHTPESIVG SYATITDWFA SFLQHGLQW PGFSSSYINQ EDILSITSLG EFKKCLLERL GYLNTQICTS SSVPTLPTVV NRPELASNYF RIVTVQQLFP K DKHFHPSD VTLDNPEVRW KHREHLAEIC KLTEQTLDAK LKTESRDHTS TADLIVFSEL AVHPEDEDIV RALAFRTRSI IF CGFVFCE QDGQIVNKAR WIIPDSSESG TQWRVRDQGK FHMTSGEMSL GVHGYRPSQH IISIEGHTEG PFKLTGAICY DAT DIKLAA DLRDLTDMFV IAAYNKDVDT FDNMASALQW HMYQHVIITN TGEYGGSTMQ APYKEKHHKL ISHAHGTGQI AIST ADIDL AAFRRKIKEY KKTKTQPAGF KRKH

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Macromolecule #2: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AF2 model of a DRT1 tetramer
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 140634
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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