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- EMDB-63214: cryo-EM structure of retron Eco2 -

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Basic information

Entry
Database: EMDB / ID: EMD-63214
Titlecryo-EM structure of retron Eco2
Map data
Sample
  • Complex: retron Eco2
    • Protein or peptide: Retron Ec67 protein
    • DNA: DNA (67-MER)
    • RNA: RNA (62-MER)
    • RNA: RNA (5'-R(*GP*UP*GP*CP*CP*UP*GP*CP*AP*UP*GP*CP*GP*U)-3')
    • DNA: DNA (5'-D(P*GP*GP*A)-3')
KeywordsRNA-mediated retron Eco2 oligomerization / RNA BINDING PROTEIN/DNA/RNA / RNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


ribonuclease H / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / defense response to virus / RNA binding / metal ion binding
Similarity search - Function
: / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang YJ / Wang C / Guan ZY / Zou TT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2025
Title: Structural basis of the RNA-mediated Retron-Eco2 oligomerization.
Authors: Yanjing Wang / Chen Wang / Yongqi Yin / Yongqing Cui / Zhikang Dai / Chang Liu / Yanke Chen / Zeyuan Guan / Tingting Zou /
Abstract: In the evolutionary arms race between bacteria and viruses, retrons have emerged as distinctive antiphage defense systems. Here, we elucidate the structure and function of Retron-Eco2, which ...In the evolutionary arms race between bacteria and viruses, retrons have emerged as distinctive antiphage defense systems. Here, we elucidate the structure and function of Retron-Eco2, which comprises a non-coding RNA (ncRNA) that encodes multicopy single-stranded DNA (msDNA, a DNA‒RNA hybrid) and a fusion protein containing a reverse transcriptase (RT) domain and a topoisomerase-primase-like (Toprim) effector domain. The Eco2 msDNA and RT-Toprim fusion protein form a 1:1 stoichiometric nucleoprotein complex that further assembles into a trimer (msDNA:RT-Toprim ratio of 3:3) with a distinctive triangular configuration. The RNA portion of the msDNA in one protomer closely intertwines around the RT domain of an adjacent protomer, mediating the formation of this self-inhibitory assembly. Upon activation, the Toprim effector domain exhibits RNase activity, degrading RNA to arrest phage replication. We further reveal that phage mutants evading Eco2-mediated defense harbor mutations in the endonuclease IV-like protein DenB, underscoring DenB's critical role in triggering the activation of this system. Together, these findings provide key structural and functional insights into Retron-Eco2, laying the groundwork for harnessing its potential in biotechnology and synthetic biology applications.
History
DepositionJan 18, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63214.png

Downloads & links

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Map

FileDownload / File: emd_63214.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-4.048504 - 6.3542805
Average (Standard dev.)0.0021104785 (±0.14880377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63214_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_63214_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 Eco2

EntireName: retron Eco2
Components
  • Complex: retron Eco2
    • Protein or peptide: Retron Ec67 protein
    • DNA: DNA (67-MER)
    • RNA: RNA (62-MER)
    • RNA: RNA (5'-R(*GP*UP*GP*CP*CP*UP*GP*CP*AP*UP*GP*CP*GP*U)-3')
    • DNA: DNA (5'-D(P*GP*GP*A)-3')

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Supramolecule #1: retron Eco2

SupramoleculeName: retron Eco2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Retron Ec67 protein

MacromoleculeName: Retron Ec67 protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 68.673102 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTKTSKLDAL RAATSREDLA KILDVKLVFL TNVLYRIGSD NQYTQFTIPK KGKGVRTISA PTDRLKDIQR RICDLLSDCR DEIFAIRKI SNNYSFGFER GKSIILNAYK HRGKQIILNI DLKDFFESFN FGRVRGYFLS NQDFLLNPVV ATTLAKAACY N GTLPQGSP ...String:
MTKTSKLDAL RAATSREDLA KILDVKLVFL TNVLYRIGSD NQYTQFTIPK KGKGVRTISA PTDRLKDIQR RICDLLSDCR DEIFAIRKI SNNYSFGFER GKSIILNAYK HRGKQIILNI DLKDFFESFN FGRVRGYFLS NQDFLLNPVV ATTLAKAACY N GTLPQGSP CSPIISNLIC NIMDMRLAKL AKKYGCTYSR YADDITISTN KNTFPLEMAT VQPEGVVLGK VLVKEIENSG FE INDSKTR LTYKTSRQEV TGLTVNRIVN IDRCYYKKTR ALAHALYRTG EYKVPDENGV LVSGGLDKLE GMFGFIDQVD KFN NIKKKL NKQPDRYVLT NATLHGFKLK LNAREKAYSK FIYYKFFHGN TCPTIITEGK TDRIYLKAAL HSLETSYPEL FREK TDSKK KEINLNIFKS NEKTKYFLDL SGGTADLKKF VERYKNNYAS YYGSVPKQPV IMVLDNDTGP SDLLNFLRNK VKSCP DDVT EMRKMKYIHV FYNLYIVLTP LSPSGEQTSM EDLFPKDILD IKIDGKKFNK NNDGDSKTEY GKHIFSMRVV RDKKRK IDF KAFCCIFDAI KDIKEHYKLM LNSLEHHHHH HHH

UniProtKB: Retron Ec67 protein

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Macromolecule #2: DNA (67-MER)

MacromoleculeName: DNA (67-MER) / type: dna / ID: 2
Details: the correct sequence is: TCCTTCGCACAGCACACCTGCCGTATAGCTCTGAATCAAGGATTTTAGGGAGGCGATTCCTCCTGCC.
Number of copies: 3 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.522113 KDa
SequenceString: (DT)(DC)(DC)(DT)(DT)(DC)(DG)(DC)(DA)(DC) (DA)(DG)(DC)(DA)(DC)(DA)(DC)(DC)(DT)(DG) (DC)(DC)(DG)(DT)(DA)(DT)(DA)(DG)(DC) (DT)(DC)(DT)(DG)(DA)(DA)(DT)(DC)(DA)(DA) (DG) (DG)(DA)(DT)(DT)(DT)(DT) ...String:
(DT)(DC)(DC)(DT)(DT)(DC)(DG)(DC)(DA)(DC) (DA)(DG)(DC)(DA)(DC)(DA)(DC)(DC)(DT)(DG) (DC)(DC)(DG)(DT)(DA)(DT)(DA)(DG)(DC) (DT)(DC)(DT)(DG)(DA)(DA)(DT)(DC)(DA)(DA) (DG) (DG)(DA)(DT)(DT)(DT)(DT)(DA)(DG) (DG)(DG)(DA)(DG)(DG)(DC)(DG)(DA)(DT)(DT) (DC)(DC) (DT)(DC)(DC)(DT)(DG)(DC)(DC)

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Macromolecule #5: DNA (5'-D(P*GP*GP*A)-3')

MacromoleculeName: DNA (5'-D(P*GP*GP*A)-3') / type: dna / ID: 5 / Number of copies: 3 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 926.661 Da
SequenceString:
(DG)(DG)(DA)

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Macromolecule #3: RNA (62-MER)

MacromoleculeName: RNA (62-MER) / type: rna / ID: 3 / Number of copies: 3
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.075932 KDa
SequenceString:
CACGCAUGUA GGCAGAUUUG UUGGUUGUGA AUCGCAACCA GUGGCCUUAA UGGCAGGAGG AA

GENBANK: GENBANK: M55249.1

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Macromolecule #4: RNA (5'-R(*GP*UP*GP*CP*CP*UP*GP*CP*AP*UP*GP*CP*GP*U)-3')

MacromoleculeName: RNA (5'-R(*GP*UP*GP*CP*CP*UP*GP*CP*AP*UP*GP*CP*GP*U)-3')
type: rna / ID: 4 / Number of copies: 3
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 4.455668 KDa
SequenceString:
GUGCCUGCAU GCGU

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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: 1.8 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 574158
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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