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- EMDB-70091: Ec83 Retron PtuAB mutant complex -

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Basic information

Entry
Database: EMDB / ID: EMD-70091
TitleEc83 Retron PtuAB mutant complex
Map dataEc83 PtuA-PtuB (2:1) complex
Sample
  • Complex: Ec83 PtuAB complex
    • Protein or peptide: Retron Ec83 probable ATPase
    • Protein or peptide: Retron Ec83 putative HNH endonuclease
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
Keywordsretron / PtuA / PtuB / ATPase / HNH nuclease / immune system
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, group 15 / AAA ATPase domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Retron Ec83 putative HNH endonuclease / Retron Ec83 probable ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang C / Rish A / Fu TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
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
DepositionApr 8, 2025-
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_70091.png

Downloads & links

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Map

FileDownload / File: emd_70091.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEc83 PtuA-PtuB (2:1) complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 280 pix.
= 305.2 Å		1.09 Å/pix.
x 280 pix.
= 305.2 Å		1.09 Å/pix.
x 280 pix.
= 305.2 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: 0.0284
Minimum - Maximum-0.027528076 - 2.2886608
Average (Standard dev.)0.00078270066 (±0.021023674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 305.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70091_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_70091_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 : Ec83 PtuAB complex

EntireName: Ec83 PtuAB complex
Components
  • Complex: Ec83 PtuAB complex
    • Protein or peptide: Retron Ec83 probable ATPase
    • Protein or peptide: Retron Ec83 putative HNH endonuclease
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Ec83 PtuAB complex

SupramoleculeName: Ec83 PtuAB 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 Ec83 probable ATPase

MacromoleculeName: Retron Ec83 probable ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 61.665863 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEQNLPSRIT KLIKKSESGD FASSYQLYKV FGSKEYGVEP DEKMSDYFKE LSAKQLEGGQ LRVADIHLEN YKGFESLIMD FSMKKNSTI LVGNNGCGKS TILDAIQKGL THLSSRLSTR SHNGDGIEKH ELRKGQNYAS IAINYDYMGI RFPMIIATTE P GYEDRAKS ...String:
MEQNLPSRIT KLIKKSESGD FASSYQLYKV FGSKEYGVEP DEKMSDYFKE LSAKQLEGGQ LRVADIHLEN YKGFESLIMD FSMKKNSTI LVGNNGCGKS TILDAIQKGL THLSSRLSTR SHNGDGIEKH ELRKGQNYAS IAINYDYMGI RFPMIIATTE P GYEDRAKS NYSGINELGS IFKTAHSINP NVSFPLIAMY TVERANDVST RDIENSEEIK EAQIWDKFKA YNKSLTGKAD FK LFFRWFK ELIEIENSDN ADITALRAEI RAKEKDLDNP LLKALLAENK NSETTKKLLE DHQNSLKVLK EKLNSYYSVN SKT LHTVED AMYSFLPGFS NLKLQRAPLD LIVDKNNVSL SVLQLSQGEK TILALIADIA RRLTLLNPNS VNPLDGTGIV LIAA IDLHL HPSWQQNIIP RLEKTFKNIQ FIVTTHSPQV CHTIDSQNIW LLKNGQKFKA PKGVRGAISS WVLENLFEVA QRPPE DKYT KLLQEYKNLV FSEKYASEDA RKLGATLSQH FGPDDETLVE LKLEIEKRIW EDDFEKDQ

UniProtKB: Retron Ec83 probable ATPase

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Macromolecule #2: Retron Ec83 putative HNH endonuclease

MacromoleculeName: Retron Ec83 putative HNH endonuclease / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.166254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MILKRINKTA EDQFLINFKA QNPNGTWDEF RNHEQGILYK RLKQHICNDQ MYLCAYCEID LDRENEHEIK VEAFKSKSGS LPGGSNWHL EWSNLLAVCL GGTNTGDDFE LPANLSCDSY KSHYEDKNKI NDKDWTGKIL LPLTLPDAHN FFTFEKVTGK L LPNESYCN ...String:
MILKRINKTA EDQFLINFKA QNPNGTWDEF RNHEQGILYK RLKQHICNDQ MYLCAYCEID LDRENEHEIK VEAFKSKSGS LPGGSNWHL EWSNLLAVCL GGTNTGDDFE LPANLSCDSY KSHYEDKNKI NDKDWTGKIL LPLTLPDAHN FFTFEKVTGK L LPNESYCN TISIDGKPAA ETLSIVTKTI EVLNLNCSRL NNARRKLLFH FNNCARERNL RKLHNLLLQW NQGEPKFFQT TR DIIIRDD RICQGLLNGT IRY

UniProtKB: Retron Ec83 putative HNH endonuclease

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / 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 #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / 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 (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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 965923
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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