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- EMDB-76002: Composite cryo-EM map of the resting EcDRT3 complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-76002
TitleComposite cryo-EM map of the resting EcDRT3 complex
Map data
Sample
  • Complex: DRT3 hexametric complex
KeywordsDRT3-ncRNA complex / reverse transcriptase / Anti-phage complex / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsDeng P / Gao A
Funding support United States, 1 items
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
DepositionMar 11, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76002.png

Downloads & links

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Map

FileDownload / File: emd_76002.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.93 Å/pix.
x 350 pix.
= 325.99 Å		0.93 Å/pix.
x 350 pix.
= 325.99 Å		0.93 Å/pix.
x 350 pix.
= 325.99 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9314 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.67
Minimum - Maximum-43.162148000000002 - 69.703963999999999
Average (Standard dev.)0.06795198 (±1.9145625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 325.99 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DRT3 hexametric complex

EntireName: DRT3 hexametric complex
Components
  • Complex: DRT3 hexametric complex

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Supramolecule #1: DRT3 hexametric complex

SupramoleculeName: DRT3 hexametric complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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: NONE / Details: Ab-initial in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 63349
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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