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- PDB-9x94: Apo Retron-Eco8 complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9x94
TitleApo Retron-Eco8 complex
Components
  • DNA (75-MER)
  • RNA (81-MER)
  • Retron Eco8 OLD nuclease
  • Retron Eco8 reverse transcriptase
KeywordsRNA BINDING PROTEIN/RNA/DNA / complex / 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
: / DNA / DNA (> 10) / RNA / RNA (> 10) / Retron Eco8 OLD nuclease / Retron Eco8 reverse transcriptase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsYu, Y. / Chen, Q.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retron Eco8 reverse transcriptase
B: Retron Eco8 OLD nuclease
C: RNA (81-MER)
D: DNA (75-MER)
E: Retron Eco8 reverse transcriptase
F: Retron Eco8 OLD nuclease
G: RNA (81-MER)
H: DNA (75-MER)
I: Retron Eco8 reverse transcriptase
J: Retron Eco8 OLD nuclease
K: RNA (81-MER)
L: DNA (75-MER)
M: Retron Eco8 reverse transcriptase
N: Retron Eco8 OLD nuclease
O: RNA (81-MER)
P: DNA (75-MER)


Theoretical massNumber of molelcules
Total (without water)719,04116
Polymers719,04116
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Retron Eco8 reverse transcriptase / RT


Mass: 43273.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ret, ERS139198_01421, Ga0119705_103345 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DV59, RNA-directed DNA polymerase
#2: Protein
Retron Eco8 OLD nuclease


Mass: 87373.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: old, ERS139198_01420, Ga0119705_103344 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DV58, Hydrolases; Acting on ester bonds
#3: RNA chain
RNA (81-MER)


Mass: 25986.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli / References: GenBank: 1881611662
#4: DNA chain
DNA (75-MER)


Mass: 23126.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 1881611662
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Apo Retron-Eco8 complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4841 nm / Nominal defocus min: 304 nm
Image recordingElectron dose: 56.58 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.15.2_3472model refinement
13Coot3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 303229 / Symmetry type: POINT
RefinementHighest resolution: 2.57 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00446697
ELECTRON MICROSCOPYf_angle_d0.70364905
ELECTRON MICROSCOPYf_dihedral_angle_d22.50810319
ELECTRON MICROSCOPYf_chiral_restr0.0447466
ELECTRON MICROSCOPYf_plane_restr0.0076655

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