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- EMDB-71270: The cryo-EM map of Retron_Eco8 complex in Apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-71270
TitleThe cryo-EM map of Retron_Eco8 complex in Apo state
Map data
Sample
  • Complex: The structure of Retron Eco8 complex
Keywordsanti-phage / bacterial immunity / retron / DNA / RNA / reverse transcription / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsYu C / Wang C / Fu T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol Cell / Year: 2025
Title: Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity.
Authors: Chengzhi Yu / Chen Wang / Taylor Forman / Jiale Xie / Samantha Major / Matthew X Fang / Jewel E Voyer / Joe Pogliano / Tian-Min Fu /
Abstract: Retrons are antiphage defense systems that synthesize multicopy single-stranded DNA (msDNA) and are being adapted for genome engineering. The Escherichia coli retron Eco8 system comprises a reverse ...Retrons are antiphage defense systems that synthesize multicopy single-stranded DNA (msDNA) and are being adapted for genome engineering. The Escherichia coli retron Eco8 system comprises a reverse transcriptase (RT), an msDNA, and an overcoming lysogenization defect (OLD)-family nuclease (Eco8-OLD), reminiscent of Gabija. Here, we present the cryo-electron microscopy structure of the Eco8 supramolecular complex, a symmetric 4:4:4 assembly of RT, Eco8-OLD, and msDNA (a hybrid of msrRNA and msdDNA). The msDNA anchors RT and Eco8-OLD into a compact architecture that traps Eco8-OLD in an autoinhibited conformation. Upon phage infection, phage single-stranded DNA-binding proteins (SSBs) bind msdDNA, inducing conformational rearrangements that relieve Eco8-OLD autoinhibition and activate its non-specific DNA nuclease activity. This structural transition enables Eco8 to mount a robust antiphage response by restricting phage genome amplification. Our findings reveal a previously unrecognized mechanism of retron activation and highlight the central role of msDNA as a molecular switch in controlling retron-mediated antiphage defense.
History
DepositionJun 16, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71270.png

Downloads & links

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Map

FileDownload / File: emd_71270.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09376447 - 0.24153133
Average (Standard dev.)-0.00004306705 (±0.008833068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71270_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_71270_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 : The structure of Retron Eco8 complex

EntireName: The structure of Retron Eco8 complex
Components
  • Complex: The structure of Retron Eco8 complex

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Supramolecule #1: The structure of Retron Eco8 complex

SupramoleculeName: The structure of Retron Eco8 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 421879
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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