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- EMDB-75826: Cryo-EM map of Drt3a and ncRNA in the elongating EcDRT3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-75826
TitleCryo-EM map of Drt3a and ncRNA in the elongating EcDRT3 complex
Map dataThe pixel size has been recalibrated.
Sample
  • Complex: Cryo-EM structure of the elongating EcDRT3 complex with Drt3a and ncRNA
KeywordsDRT3-ncRNA complex / reverse transcriptase / Anti-phage complex / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 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 3, 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_75826.png

Downloads & links

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Map

FileDownload / File: emd_75826.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe pixel size has been recalibrated.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 560 pix.
= 470.904 Å		0.84 Å/pix.
x 560 pix.
= 470.904 Å		0.84 Å/pix.
x 560 pix.
= 470.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8409 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-5.220476 - 5.572529
Average (Standard dev.)0.0001677615 (±0.016635703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 470.904 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_75826_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75826_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the elongating EcDRT3 complex with Drt3a and...

EntireName: Cryo-EM structure of the elongating EcDRT3 complex with Drt3a and ncRNA
Components
  • Complex: Cryo-EM structure of the elongating EcDRT3 complex with Drt3a and ncRNA

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Supramolecule #1: Cryo-EM structure of the elongating EcDRT3 complex with Drt3a and...

SupramoleculeName: Cryo-EM structure of the elongating EcDRT3 complex with Drt3a and ncRNA
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: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 1438752
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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