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- EMDB-65064: cryoEM structure of retron-Eco7 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65064
TitlecryoEM structure of retron-Eco7 complex
Map data
Sample
  • Complex: retron-Eco7 complex
    • Protein or peptide: Retron Ec78 reverse transcriptase
    • Protein or peptide: Retron Ec78 probable ATPase
    • Protein or peptide: Retron Ec78 putative HNH endonuclease
    • RNA: msrRNA
    • DNA: msdDNA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsretron-Eco7 / toxin-antitoxin / DNA BINDING PROTEIN/RNA/DNA / DNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / endonuclease activity / defense response to virus / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. ...: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Retron Ec78 probable ATPase / Retron Ec78 putative HNH endonuclease / Retron Ec78 reverse transcriptase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDai ZK / Wang YJ / Guan ZY / Zou TT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Phage nuclease-mediated defense activation of the bacterial Retron-Eco7 toxin-antitoxin system.
Authors: Zhikang Dai / Chang Liu / Yanjing Wang / Xueting Chen / Xiaofang Fu / Kaiyue Yang / Rui Zhu / Xianyue Jia / Yanke Chen / Pan Tao / Zeyuan Guan / Tingting Zou /
Abstract: Retrons are bacterial antiphage defense systems comprising a reverse transcriptase (RT), a non-coding RNA (ncRNA), and cognate effector proteins. The RT synthesizes multicopy single-stranded DNA ...Retrons are bacterial antiphage defense systems comprising a reverse transcriptase (RT), a non-coding RNA (ncRNA), and cognate effector proteins. The RT synthesizes multicopy single-stranded DNA (msDNA) from the ncRNA template to detect phage invasion. This study focuses on Retron-Eco7, which integrates retron-based sensing with the effector module of Septu-a characterized antiphage system in which the PtuAB complex mediates nuclease-dependent defense. However, the activation mechanism of this hybrid system remains unclear. Here, we determined cryo-electron microscopy structures of the RT-msDNA-PtuAB quaternary complex and the PtuAB binary complex in Retron-Eco7. Structural analyses reveal that the DNA stem-loop of msDNA extensively interacts with PtuA subunits via electrostatic interactions. We establish Retron-Eco7 as a novel toxin-antitoxin system, in which RT-msDNA acts as the antitoxin, directly binding and neutralizing the PtuAB toxin. Furthermore, we identified a phage-encoded flap endonuclease as a trigger for Retron-Eco7 activation, which cleaves msDNA to release the PtuAB toxin. Our findings demonstrate the diversity in bacterial retron defense systems and uncover a novel activation mechanism of the Septu-derived retron toxin-antitoxin system.
History
DepositionJun 16, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65064.png

Downloads & links

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Map

FileDownload / File: emd_65064.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.)
0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.309672 - 3.7721367
Average (Standard dev.)-0.0005664904 (±0.07022391)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65064_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65064_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-Eco7 complex

EntireName: retron-Eco7 complex
Components
  • Complex: retron-Eco7 complex
    • Protein or peptide: Retron Ec78 reverse transcriptase
    • Protein or peptide: Retron Ec78 probable ATPase
    • Protein or peptide: Retron Ec78 putative HNH endonuclease
    • RNA: msrRNA
    • DNA: msdDNA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: retron-Eco7 complex

SupramoleculeName: retron-Eco7 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Retron Ec78 reverse transcriptase

MacromoleculeName: Retron Ec78 reverse transcriptase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.629242 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSVIRRLAAV LRQSDSGISA FLVTAPRKYK VYKIPKRTTG FRVIAQPAKG LKDIQRAFVQ LYNFPVHDAS MAYMKGKGIR DNAAAHAGN QYLLKADLED FFNSITPAIF WRCIEMSSAL TPQFEPQDKF FIEKILFWQP IKHRKTKLIL SVGAPSSPVI S NFCMYEFD ...String:
MSVIRRLAAV LRQSDSGISA FLVTAPRKYK VYKIPKRTTG FRVIAQPAKG LKDIQRAFVQ LYNFPVHDAS MAYMKGKGIR DNAAAHAGN QYLLKADLED FFNSITPAIF WRCIEMSSAL TPQFEPQDKF FIEKILFWQP IKHRKTKLIL SVGAPSSPVI S NFCMYEFD NRIHAACNKL EITYTRYADD LTFSCNIPNV LKAVPSTIEA LLKDLFGSEL RLNHSKTVFS SKAHNRHVTG VT INNEETL SLGRDRKRFI KHLINQYKYG LLDNEDKAYL TGLLAFASHI EPGFITRMNE KYSLELMERL RGQR

UniProtKB: Retron Ec78 reverse transcriptase

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Macromolecule #2: Retron Ec78 probable ATPase

MacromoleculeName: Retron Ec78 probable ATPase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.466625 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTKQYERKAK GGNLLSAFEL YQRNTDNMPG LGEMLVDEWF ETCRDYIQDG HVDESGTFRP DNAFYLRRLT LKDFRRFSLL EIKFEEDLT VIIGNNGKGK TSILYAIAKT LSWFVANILK EGGSGQRLSE LTDIKNDAEN RYADVSSTFF FGKGLKSVPI R LSRSALGT ...String:
MTKQYERKAK GGNLLSAFEL YQRNTDNMPG LGEMLVDEWF ETCRDYIQDG HVDESGTFRP DNAFYLRRLT LKDFRRFSLL EIKFEEDLT VIIGNNGKGK TSILYAIAKT LSWFVANILK EGGSGQRLSE LTDIKNDAEN RYADVSSTFF FGKGLKSVPI R LSRSALGT AERRDSEVKP ARDLADIWRV INEAKTINLP TFALYNVERS QPFNRNTKDN AGRREERFDA YSQALGGAGR FD HFVEWYI YLHKRTISDI SSSIKELEQQ VNDLQRSVDG GMVSVKSLLE QMKLKLSEAS ERNDAAVSSK MVTESVQKSI VEK SICSVV PSISKIWVEM TTGSDLVKVT NDGHDVTIDQ LSDGQRVFLS LVADLARRMV MLNPLLENPL EGRGIVLIDE IELH LHPKW QQEVILNLRS VFPNIQFIIT THSPIVLSTI EKRCIREFDP NDDGNQSFLD SPDMQTKGSE NAQILEQVMN VHPTP PGIA ESHWLGDFEL LLLDNSGELD NQSQELYDKI KTHFGIDSAE LKKADSLIRI NKMKNKINKI RAEKGK

UniProtKB: Retron Ec78 probable ATPase

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Macromolecule #3: Retron Ec78 putative HNH endonuclease

MacromoleculeName: Retron Ec78 putative HNH endonuclease / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.816848 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKELARLESP EILDQYTAGQ NDWMEIDQSA VWPKLTEMQG EFCAYCECRL NRRHIEHFRP RGKFPALTFI WSNLFGSCGD SKKSGGWSR CGIYKDNGAG AYNADDLIKP DEENPDDYLL FLTTGEVVPA IGLTGRALKK AQETIRVFNL NGDIKLLGSR R TAVQAIMP ...String:
MKELARLESP EILDQYTAGQ NDWMEIDQSA VWPKLTEMQG EFCAYCECRL NRRHIEHFRP RGKFPALTFI WSNLFGSCGD SKKSGGWSR CGIYKDNGAG AYNADDLIKP DEENPDDYLL FLTTGEVVPA IGLTGRALKK AQETIRVFNL NGDIKLLGSR R TAVQAIMP NVEYLYSLLE EFEEDDWNEM LRDELEKIES DEFKTALKHA WTSNQEFA

UniProtKB: Retron Ec78 putative HNH endonuclease

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Macromolecule #4: msrRNA

MacromoleculeName: msrRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.813266 KDa
SequenceString:
ACUCUUUAGC GUUGGACGGU UACGUCUAGU CGGGUGAUUA GCCAGACUCU AACUUAUUGA ACGUA

GENBANK: GENBANK: U02551.1

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Macromolecule #5: msdDNA

MacromoleculeName: msdDNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.869648 KDa
SequenceString: (DG)(DG)(DA)(DA)(DG)(DC)(DG)(DA)(DA)(DA) (DG)(DT)(DG)(DT)(DC)(DG)(DC)(DA)(DA)(DC) (DC)(DC)(DG)(DA)(DG)(DA)(DG)(DA)(DG) (DG)(DA)(DA)(DC)(DG)(DA)(DT)(DC)(DT)(DC) (DG) (DG)(DG)(DT)(DT)(DG)(DC) ...String:
(DG)(DG)(DA)(DA)(DG)(DC)(DG)(DA)(DA)(DA) (DG)(DT)(DG)(DT)(DC)(DG)(DC)(DA)(DA)(DC) (DC)(DC)(DG)(DA)(DG)(DA)(DG)(DA)(DG) (DG)(DA)(DA)(DC)(DG)(DA)(DT)(DC)(DT)(DC) (DG) (DG)(DG)(DT)(DT)(DG)(DC)(DG)(DA) (DC)(DA)(DC)(DT)(DT)(DT)(DC)(DG)(DC)(DA) (DA)(DC) (DC)(DC)(DT)(DT)(DA)(DA)(DT) (DA)(DC)(DG)(DT)(DT)(DC)(DA)

GENBANK: GENBANK: U02551.1

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / 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 stateparticle

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Sample preparation

BufferpH: 8
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: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 413082
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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