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- EMDB-47737: 4-component structure of retron Ec83 -

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Basic information

Entry
Database: EMDB / ID: EMD-47737
Title4-component structure of retron Ec83
Map dataFlipped along the z-axis relative to half maps
Sample
  • Complex: Complete Ec83 retron complex
    • Protein or peptide: Retron Ec83 probable ATPase
    • Protein or peptide: Retron Ec83 putative HNH endonuclease
    • Protein or peptide: Retron Ec83 reverse transcriptase
    • DNA: DNA (79-MER), msDNA
    • RNA: RNA (38-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
KeywordsATPase / HNH-Endonuclease / Retron / msDNA / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / RNA-directed DNA polymerase activity / RNA-directed DNA polymerase / 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 / RNA-directed DNA polymerase (reverse transcriptase), msDNA / AAA domain, group 15 / AAA ATPase domain / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / ATPases associated with a variety of cellular activities ...: / Retron Ec78 putative HNH endonuclease-like / RNA-directed DNA polymerase (reverse transcriptase), msDNA / AAA domain, group 15 / AAA ATPase domain / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Retron Ec83 putative HNH endonuclease / Retron Ec83 reverse transcriptase / Retron Ec83 probable ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsRish AD / Wang C / Fu TM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GR128399 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31AI181575-01 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_47737.png

Downloads & links

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Map

FileDownload / File: emd_47737.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFlipped along the z-axis relative to half maps
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-0.032860015 - 2.0728004
Average (Standard dev.)0.0014506694 (±0.025972845)
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: Same orientation as main map

Fileemd_47737_half_map_1.map
AnnotationSame orientation as main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Same orientation as main map

Fileemd_47737_half_map_2.map
AnnotationSame orientation as main 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 : Complete Ec83 retron complex

EntireName: Complete Ec83 retron complex
Components
  • Complex: Complete Ec83 retron complex
    • Protein or peptide: Retron Ec83 probable ATPase
    • Protein or peptide: Retron Ec83 putative HNH endonuclease
    • Protein or peptide: Retron Ec83 reverse transcriptase
    • DNA: DNA (79-MER), msDNA
    • RNA: RNA (38-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Complete Ec83 retron complex

SupramoleculeName: Complete Ec83 retron 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 Ec83 probable ATPase

MacromoleculeName: Retron Ec83 probable ATPase / type: protein_or_peptide / ID: 1 / Details: ATPase / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 61.767902 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 LIDE 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 / Details: HNH-endonuclease / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.233324 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MILKRINKTA EDQFLINFKA QNPNGTWDEF RNHEQGILYK RLKQHICNDQ MYLCAYCEID LDRENEHEIK VEHFKSKSGS LPGGSNWHL EWSNLLAVCL GGTNTGDDFE LPANLSCDSY KSHYEDKNKI NDKDWTGKIL LPLTLPDAHN FFTFEKVTGK L LPNESYCN ...String:
MILKRINKTA EDQFLINFKA QNPNGTWDEF RNHEQGILYK RLKQHICNDQ MYLCAYCEID LDRENEHEIK VEHFKSKSGS 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: Retron Ec83 reverse transcriptase

MacromoleculeName: Retron Ec83 reverse transcriptase / type: protein_or_peptide / ID: 3 / Details: RT / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.794352 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSIDIETTLQ KAYPDFDVLL KSRPATHYKV YKIPKRTIGY RIIAQPTPRV KAIQRDIIEI LKQHTHIHDA ATAYVDGKNI LDNAKIHQS SVYLLKLDLV NFFNKITPEL LFKALARQKV DISDTNKNLL KQFCFWNRTK RKNGALVLSV GAPSSPFISN I VMSSFDEE ...String:
MSIDIETTLQ KAYPDFDVLL KSRPATHYKV YKIPKRTIGY RIIAQPTPRV KAIQRDIIEI LKQHTHIHDA ATAYVDGKNI LDNAKIHQS SVYLLKLDLV NFFNKITPEL LFKALARQKV DISDTNKNLL KQFCFWNRTK RKNGALVLSV GAPSSPFISN I VMSSFDEE ISSFCKENKI SYSRYADDLT FSTNERDVLG LAHQKVKTTL IRFFGTRIII NNNKIVYSSK AHNRHVTGVT LT NNNKLSL GRERKRYITS LVFKFKEGKL SNVDINHLRG LIGFAYNIEP AFIERLEKKY GESTIKSIKK YSEGG

UniProtKB: Retron Ec83 reverse transcriptase

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Macromolecule #4: DNA (79-MER), msDNA

MacromoleculeName: DNA (79-MER), msDNA / type: dna / ID: 4 / Details: msDNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.559391 KDa
SequenceString: (DT)(DT)(DG)(DA)(DA)(DG)(DC)(DC)(DG)(DC) (DG)(DG)(DA)(DA)(DC)(DA)(DA)(DA)(DC)(DT) (DT)(DT)(DT)(DT)(DG)(DA)(DT)(DC)(DC) (DG)(DC)(DA)(DA)(DC)(DC)(DT)(DA)(DC)(DT) (DG) (DG)(DA)(DT)(DT)(DG)(DC) ...String:
(DT)(DT)(DG)(DA)(DA)(DG)(DC)(DC)(DG)(DC) (DG)(DG)(DA)(DA)(DC)(DA)(DA)(DA)(DC)(DT) (DT)(DT)(DT)(DT)(DG)(DA)(DT)(DC)(DC) (DG)(DC)(DA)(DA)(DC)(DC)(DT)(DA)(DC)(DT) (DG) (DG)(DA)(DT)(DT)(DG)(DC)(DG)(DG) (DC)(DT)(DC)(DA)(DA)(DA)(DA)(DA)(DG)(DT) (DT)(DT) (DG)(DT)(DT)(DC)(DC)(DG)(DC) (DA)(DA)(DC)(DT)(DG)(DT)(DA)(DA)(DA)(DT) (DG)(DT)(DA) (DA)(DT)(DC)

GENBANK: GENBANK: Z12832.1

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Macromolecule #5: RNA (38-MER)

MacromoleculeName: RNA (38-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.102132 KDa
SequenceString:
GUUGGGCGUU GCGCCAAACU CUAAUUUAUU GAUUACAU

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / 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: 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: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80872
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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