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- EMDB-66659: Apo Retron-Eco8 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-66659
TitleApo Retron-Eco8 complex
Map data
Sample
  • Complex: Apo Retron-Eco8 complex
    • Protein or peptide: Retron Eco8 reverse transcriptase
    • Protein or peptide: Retron Eco8 OLD nuclease
    • RNA: RNA (81-MER)
    • DNA: DNA (75-MER)
Keywordscomplex / RNA BINDING PROTEIN/RNA/DNA / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


nuclease activity / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / defense response to virus / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
AAA domain, putative AbiEii toxin, Type IV TA system / : / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Retron Eco8 OLD nuclease / Retron Eco8 reverse transcriptase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsYu Y / Chen Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structural basis of Retron-Eco8-mediated antiphage defense.
Authors: Chao Xiong / Huan Pu / Yiwen Tang / Ting Liu / Dantong Luo / Qiang Chen / Yamei Yu /
Abstract: Retrons represent a novel class of bacterial defense systems that employ reverse transcriptase (RT), noncoding RNA, and effector proteins to counteract phage infections. In this study, we elucidate ...Retrons represent a novel class of bacterial defense systems that employ reverse transcriptase (RT), noncoding RNA, and effector proteins to counteract phage infections. In this study, we elucidate the molecular mechanism of a retron system, Retron-Eco8. Biochemical experiments reveal that the Retron-Eco8 holocomplex, rather than the effector alone, exhibits double-stranded DNA cleavage activity, triggering abortive infection and therefore effectively halting phage propagation. Cryo-electron microscopy (cryo-EM) analysis reveals a supramolecular assembly comprising four RT subunits, four multicopy single-stranded DNA molecules, and four overcoming lysogenization defect (OLD) nucleases-a configuration critical for antiphage defense. Notably, we examine the activation of Retron-Eco8 by diverse single-stranded DNA-binding (SSB) proteins, and phylogenetic analysis of these SSB proteins elucidates the phage resistance specificity. Collectively, our findings delineate the structural architecture of the Retron-Eco8 defense complex and provide mechanistic insights into retron-mediated bacterial immunity.
History
DepositionOct 20, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66659.png

Downloads & links

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Map

FileDownload / File: emd_66659.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.139
Minimum - Maximum-0.18041784 - 3.1271234
Average (Standard dev.)0.0012575932 (±0.029149603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66659_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_66659_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 : Apo Retron-Eco8 complex

EntireName: Apo Retron-Eco8 complex
Components
  • Complex: Apo Retron-Eco8 complex
    • Protein or peptide: Retron Eco8 reverse transcriptase
    • Protein or peptide: Retron Eco8 OLD nuclease
    • RNA: RNA (81-MER)
    • DNA: DNA (75-MER)

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Supramolecule #1: Apo Retron-Eco8 complex

SupramoleculeName: Apo Retron-Eco8 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Retron Eco8 reverse transcriptase

MacromoleculeName: Retron Eco8 reverse transcriptase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.273203 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKTKKMILVD KVFYEKILSV ESFKENIITQ SAIPKISNKE VRLISSGSKI FYAINNTSPH SHVQLRLNRF FLSHIPLNSA AKAFVRGGS YLKYLEPHIY GSSYCRLDIS SFFNNISFDD VKQSLSPYIK DEYLIGTEQK LIDAILNSVG YESPIRKDKG M IIPMGFRT ...String:
MKTKKMILVD KVFYEKILSV ESFKENIITQ SAIPKISNKE VRLISSGSKI FYAINNTSPH SHVQLRLNRF FLSHIPLNSA AKAFVRGGS YLKYLEPHIY GSSYCRLDIS SFFNNISFDD VKQSLSPYIK DEYLIGTEQK LIDAILNSVG YESPIRKDKG M IIPMGFRT SPAISNIVFR KMDLLIQDFC AKKGVIYSRY ADDMLFSNPR ESKLLMSDYF IDEISSLLSI MGFNINQSKY IS REKEISI NGYVIENKGG NGSIGTIRLS KSKLNTVLKV THALAQNIPY KNICNKYIKV RLKEKNIKYE SKKDEFEKKY YRD QLINYL GGYRSYLISL VKFHSEYKCV NSDFIIQING ILNDIQNHIQ KIKKNRRL

UniProtKB: Retron Eco8 reverse transcriptase

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Macromolecule #2: Retron Eco8 OLD nuclease

MacromoleculeName: Retron Eco8 OLD nuclease / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 87.373789 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTIESIRVKN LLSFDDVILR DFRDINCIIG RNNVGKSNLL KVIRYFYAKL ENKKVIPLDF HTNYNAVGEI TFTFDTTRIK KIVTSRKNN GRFHKHIYNT LFKSSSVKLN FEELIARKNS TNKSFFSLTL TICKDDSVMW SVDDPKVRSL LATLYPFLYI E TRHIDLYD ...String:
MTIESIRVKN LLSFDDVILR DFRDINCIIG RNNVGKSNLL KVIRYFYAKL ENKKVIPLDF HTNYNAVGEI TFTFDTTRIK KIVTSRKNN GRFHKHIYNT LFKSSSVKLN FEELIARKNS TNKSFFSLTL TICKDDSVMW SVDDPKVRSL LATLYPFLYI E TRHIDLYD WNPIWKLISN LNSFNFDDVD HDELVNFLDE KISSRKGDYK KYIDRVVSVI DTKPYTYKEK VINYIKVAIK GD SFVNAGE ELFTQSDGTN SNKFLETLLH LLITLTRTEF ISPIVYIDEP EVGLHPKLAE SFVSNLNKIY SKFKKTSELS GPG RYKTPY PNIFYSTHSP SILKQTIKLF GKDQQVLHFS KKKDGSTRVN KINSTYSDER FLNIFSDNEA RLFFSEYIVF VEGA TELEL FRNLSLLNLY PAFSLADIYD ANEVILANIN PGYSKASIPF VIIKDIDTLI DYSIKTEKFS LRPLFEKMIK ELTKE FDYY DTGFGRVRKE IDLFSDIQSS TKKHMDSGLF FKRFSLHNLS SRINKVSRKL NRYFMTTTIE GALINEQSLP YFFNWI GDV ILTQMTINNP NPDKFIEAMR RRYNIKSQVV PLFKSVFCIG LNHPVYSSAV DKQALRIKLS FLNYLKRKVY SDFNNEK EI VLALRLAFGG KTETQYTLDK LRKDGEAELF REKIKNYKNN ELFFLEPQMT KTSGWVTTFL NYTIEKITSE ESDDDRIR Q KLSFIFPEII SIIEQASSSI EAEESSLTG

UniProtKB: Retron Eco8 OLD nuclease

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Macromolecule #3: RNA (81-MER)

MacromoleculeName: RNA (81-MER) / type: rna / ID: 3 / Number of copies: 4
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.986383 KDa
SequenceString:
AAGCUUCUUC UUCGAUAGAA GCUGAGGAGU CCAGUUUGAC UGGAUAAGGU GUUCGCCAUC UCUAGCCUCA GUAAAAACUA G

GENBANK: GENBANK: CP057441.1

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Macromolecule #4: DNA (75-MER)

MacromoleculeName: DNA (75-MER) / type: dna / ID: 4 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.126848 KDa
SequenceString: (DC)(DA)(DA)(DG)(DA)(DC)(DC)(DA)(DA)(DT) (DC)(DT)(DT)(DT)(DA)(DC)(DA)(DC)(DT)(DC) (DT)(DG)(DT)(DG)(DA)(DG)(DT)(DA)(DT) (DT)(DA)(DA)(DA)(DG)(DT)(DT)(DA)(DC)(DC) (DT) (DA)(DT)(DA)(DG)(DC)(DG) ...String:
(DC)(DA)(DA)(DG)(DA)(DC)(DC)(DA)(DA)(DT) (DC)(DT)(DT)(DT)(DA)(DC)(DA)(DC)(DT)(DC) (DT)(DG)(DT)(DG)(DA)(DG)(DT)(DA)(DT) (DT)(DA)(DA)(DA)(DG)(DT)(DT)(DA)(DC)(DC) (DT) (DA)(DT)(DA)(DG)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DT)(DG)(DC)(DG)(DC)(DA)(DA) (DA)(DG) (DG)(DA)(DT)(DG)(DA)(DG)(DC) (DT)(DA)(DG)(DT)(DT)(DT)(DT)(DT)

GENBANK: GENBANK: CP057441.1

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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 K2 SUMMIT (4k x 4k) / Average electron dose: 56.58 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.841 µm / Nominal defocus min: 0.304 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: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 303229
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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