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- EMDB-65052: cryoEM structure of ptuA-ptuB complex in Retron-Eco7 anti-phage system -

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Basic information

Entry
Database: EMDB / ID: EMD-65052
TitlecryoEM structure of ptuA-ptuB complex in Retron-Eco7 anti-phage system
Map data
Sample
  • Complex: PtuA-PtuB complex
    • Protein or peptide: Retron Ec78 probable ATPase
    • Protein or peptide: Retron Ec78 putative HNH endonuclease
  • Ligand: ZINC ION
Keywordsretron-Eco7 / toxin-antitoxin / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / double-strand break repair / endonuclease activity / defense response to virus / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Retron Ec78 probable ATPase / Retron Ec78 putative HNH endonuclease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65052.png

Downloads & links

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Map

FileDownload / File: emd_65052.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.5592637 - 3.7899518
Average (Standard dev.)-0.000100234094 (±0.07953401)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65052_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_65052_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : PtuA-PtuB complex

EntireName: PtuA-PtuB complex
Components
  • Complex: PtuA-PtuB complex
    • Protein or peptide: Retron Ec78 probable ATPase
    • Protein or peptide: Retron Ec78 putative HNH endonuclease
  • Ligand: ZINC ION

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Supramolecule #1: PtuA-PtuB complex

SupramoleculeName: PtuA-PtuB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Retron Ec78 probable ATPase

MacromoleculeName: Retron Ec78 probable ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #2: Retron Ec78 putative HNH endonuclease

MacromoleculeName: Retron Ec78 putative HNH endonuclease / type: protein_or_peptide / ID: 2 / 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 #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 165087
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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