[English] 日本語
Yorodumi
- EMDB-69132: Cryo-EM structure of the Retron-Eco8-SSB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-69132
TitleCryo-EM structure of the Retron-Eco8-SSB complex
Map data
Sample
  • Complex: Heterotetramer Retron-Eco8-SSB complex
    • Protein or peptide: Retron Eco8 reverse transcriptase
    • Protein or peptide: Retron Eco8 OLD nuclease
    • RNA: RNA (83-MER)
    • DNA: DNA (75-MER)
KeywordsANTIVIRAL PROTEIN/DNA/RNA / ANTIVIRAL PROTEIN-DNA-RNA 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 / : / Reverse transcriptase (RNA-dependent DNA polymerase) / ATPase, AAA-type, core / 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: 3.11 Å
AuthorsZhang JT / Ji CG / Li ZL / Wei XY / Jia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Mechanistic insights into activation of bacterial Retron-Eco8 immunity by phage protein SSB.
Authors: Chao-Guang Ji / Zhuolin Li / Xin-Yang Wei / Yuelong Li / Jun-Tao Zhang / Xueyan Liu / Ning Jia /
Abstract: The Retron-Eco8 system, comprising a reverse transcriptase (RT), a non-coding RNA (ncRNA), and an OLD-family nuclease effector, protects bacteria from phage infection via abortive infection upon ...The Retron-Eco8 system, comprising a reverse transcriptase (RT), a non-coding RNA (ncRNA), and an OLD-family nuclease effector, protects bacteria from phage infection via abortive infection upon sensing a phage single-stranded DNA-binding protein (SSB). However, the molecular basis of this immunity remained unclear. Here, we report cryo-electron microscopy (cryo-EM) structures of Retron-Eco8 in inactive and activated states, revealing mechanisms of phage-triggered activation and effector function. Retron-Eco8 assembles into a tetrameric complex in which each protomer contains an RT, msrRNA-msdDNA duplex, and effector in an autoinhibited conformation. Upon phage infection, phage SSB binds msdDNA, relieving autoinhibition and activating the nuclease effector to degrade both phage and host DNA, triggering cell death to block phage propagation. Host SSB fails to activate the system, while DNA binding and oligomerization of phage SSB are essential for this activation, highlighting its specificity. These findings elucidate the molecular mechanism of Retron-Eco8-mediated immunity, facilitating retron-based biotechnological applications.
History
DepositionFeb 12, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_69132.png

Downloads & links

-
Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 560 pix.
= 469.28 Å		0.84 Å/pix.
x 560 pix.
= 469.28 Å		0.84 Å/pix.
x 560 pix.
= 469.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.838 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.643838 - 2.9386814
Average (Standard dev.)-0.000088267494 (±0.05365256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 469.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_69132_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_69132_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_69132_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Heterotetramer Retron-Eco8-SSB complex

EntireName: Heterotetramer Retron-Eco8-SSB complex
Components
  • Complex: Heterotetramer Retron-Eco8-SSB complex
    • Protein or peptide: Retron Eco8 reverse transcriptase
    • Protein or peptide: Retron Eco8 OLD nuclease
    • RNA: RNA (83-MER)
    • DNA: DNA (75-MER)

-
Supramolecule #1: Heterotetramer Retron-Eco8-SSB complex

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

-
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-Gold(DE3)pLysS AG' (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

-
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-Gold(DE3)pLysS AG' (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

-
Macromolecule #3: RNA (83-MER)

MacromoleculeName: RNA (83-MER) / type: rna / ID: 3 / Number of copies: 4
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.660795 KDa
SequenceString:
AGAAGCUUCU UCUUCGAUAG AAGCUGAGGA GUCCAGUUUG ACUGGAUAAG GUGUUCGCCA UCUCUAGCCU CAGUAAAAAC UAG

GENBANK: GENBANK: CP057441.1

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k 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: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 114917
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more