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- EMDB-47740: Retron Ec78 cryo-EM map at 3.01 A -

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Basic information

Entry
Database: EMDB / ID: EMD-47740
TitleRetron Ec78 cryo-EM map at 3.01 A
Map data
Sample
  • Complex: Retron Ec78 complex
    • Protein or peptide: Ec78 PtuA
    • Protein or peptide: Ec78 PtuB
    • Protein or peptide: Ec78 RT
KeywordsATPase / Retron / ANTIVIRAL PROTEIN / msDNA / Reverse Transcriptase / ncRNA
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsRish AD / Wang C / Fu TM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31AI181575-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GR128399 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM144293 United States
CitationJournal: Science / Year: 2025
Title: Disassembly activates Retron-Septu for antiphage defense.
Authors: Chen Wang / Anthony D Rish / Emily G Armbruster / Jiale Xie / Anna B Loveland / Zhangfei Shen / Bradley Gu / Andrei A Korostelev / Joe Pogliano / Tian-Min Fu /
Abstract: Retrons are antiphage defense systems that produce multicopy single-stranded DNA (msDNA) and hold promises for genome engineering. However, the mechanisms of defense remain unclear. The Retron-Septu ...Retrons are antiphage defense systems that produce multicopy single-stranded DNA (msDNA) and hold promises for genome engineering. However, the mechanisms of defense remain unclear. The Retron-Septu system uniquely integrates retron and Septu antiphage defenses. Cryo-electron microscopy structures reveal asymmetric nucleoprotein complexes comprising a reverse transcriptase (RT), msDNA (a hybrid of msdDNA and msrRNA), and two PtuAB copies. msdDNA and msrRNA are essential for assembling this complex, with msrRNA adopting a conserved lariat-like structure that regulates reverse transcription. Notably, the assembled Retron-Septu complex is inactive, with msdDNA occupying the PtuA DNA-binding site. Activation occurs upon disassembly, releasing PtuAB, which degrades single-stranded DNA to restrict phage replication. This "arrest-and-release" mechanism underscores the dynamic regulatory roles of msDNA, advancing our understanding of antiphage defense strategies.
History
DepositionNov 6, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47740.png

Downloads & links

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Map

FileDownload / File: emd_47740.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.02789515 - 2.1842349
Average (Standard dev.)0.0010880604 (±0.02223128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 327.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47740_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_47740_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 : Retron Ec78 complex

EntireName: Retron Ec78 complex
Components
  • Complex: Retron Ec78 complex
    • Protein or peptide: Ec78 PtuA
    • Protein or peptide: Ec78 PtuB
    • Protein or peptide: Ec78 RT

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Supramolecule #1: Retron Ec78 complex

SupramoleculeName: Retron Ec78 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Ec78 PtuA

MacromoleculeName: Ec78 PtuA / type: protein_or_peptide / ID: 1 / Details: 4 chains are present in the complex / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTKQYERKAK GGNLLSAFEL YQRNTDNMPG LGEMLVDEWF ETCRDYIQDG HVDESGTFRP DNAFYLRRLT LKDFRRFSLL EIKFEEDLTV IIGNNGKGKT SILYAIAKTL SWFVANILKE GGSGQRLSEL TDIKNDAENR YADVSSTFFF GKGLKSVPIR LSRSALGTAE ...String:
MTKQYERKAK GGNLLSAFEL YQRNTDNMPG LGEMLVDEWF ETCRDYIQDG HVDESGTFRP DNAFYLRRLT LKDFRRFSLL EIKFEEDLTV IIGNNGKGKT SILYAIAKTL SWFVANILKE GGSGQRLSEL TDIKNDAENR YADVSSTFFF GKGLKSVPIR LSRSALGTAE RRDSEVKPAR DLADIWRVIN EAKTINLPTF ALYNVERSQP FNRNTKDNAG RREERFDAYS QALGGAGRFD HFVEWYIYLH KRTISDISSS IKELEQQVND LQRSVDGGMV SVKSLLEQMK LKLSEASERN DAAVSSKMVT ESVQKSIVEK SICSVVPSIS KIWVEMTTGS DLVKVTNDGH DVTIDQLSDG QRVFLSLVAD LARRMVMLNP LLENPLEGRG IVLIDEIELH LHPKWQQEVI LNLRSVFPNI QFIITTHSPI VLSTIEKRCI REFDPNDDGN QSFLDSPDMQ TKGSENAQIL EQVMNVHPTP PGIAESHWLG DFELLLLDNS GELDNQSQEL YDKIKTHFGI DSAELKKADS LIRINKMKNK INKIRAEKGK

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Macromolecule #2: Ec78 PtuB

MacromoleculeName: Ec78 PtuB / type: protein_or_peptide / ID: 2 / Details: 2 chains are present in the complex / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKELARLESP EILDQYTAGQ NDWMEIDQSA VWPKLTEMQG EFCAYCECRL NRRHIEHFRP RGKFPALTFI WSNLFGSCGD SKKSGGWSRC GIYKDNGAGA YNADDLIKPD EENPDDYLLF LTTGEVVPAI GLTGRALKKA QETIRVFNLN GDIKLLGSRR TAVQAIMPNV ...String:
MKELARLESP EILDQYTAGQ NDWMEIDQSA VWPKLTEMQG EFCAYCECRL NRRHIEHFRP RGKFPALTFI WSNLFGSCGD SKKSGGWSRC GIYKDNGAGA YNADDLIKPD EENPDDYLLF LTTGEVVPAI GLTGRALKKA QETIRVFNLN GDIKLLGSRR TAVQAIMPNV EYLYSLLEEF EEDDWNEMLR DELEKIESDE FKTALKHAWT SNQEFA

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Macromolecule #3: Ec78 RT

MacromoleculeName: Ec78 RT / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MSVIRRLAAV LRQSDSGISA FLVTAPRKYK VYKIPKRTTG FRVIAQPAKG LKDIQRAFVQ LYNFPVHDAS MAYMKGKGIR DNAAAHAGNQ YLLKADLEDF FNSITPAIFW RCIEMSSALT PQFEPQDKFF IEKILFWQPI KHRKTKLILS VGAPSSPVIS NFCMYEFDNR ...String:
MSVIRRLAAV LRQSDSGISA FLVTAPRKYK VYKIPKRTTG FRVIAQPAKG LKDIQRAFVQ LYNFPVHDAS MAYMKGKGIR DNAAAHAGNQ YLLKADLEDF FNSITPAIFW RCIEMSSALT PQFEPQDKFF IEKILFWQPI KHRKTKLILS VGAPSSPVIS NFCMYEFDNR IHAACNKLEI TYTRYADDLT FSCNIPNVLK AVPSTIEALL KDLFGSELRL NHSKTVFSSK AHNRHVTGVT INNEETLSLG RDRKRFIKHL INQYKYGLLD NEDKAYLTGL LAFASHIEPG FITRMNEKYS LELMGRLRGQ R

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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 BIOQUANTUM (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: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215222
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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