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- PDB-9x9b: Retron-Eco8 complex with ATP-Mg2+ -

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Basic information

Entry
Database: PDB / ID: 9x9b
TitleRetron-Eco8 complex with ATP-Mg2+
Components
  • DNA (83-MER)
  • RNA (82-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 domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / 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: 2.8 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 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 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 (82-MER)
D: DNA (83-MER)
E: Retron Eco8 reverse transcriptase
F: Retron Eco8 OLD nuclease
G: RNA (82-MER)
H: DNA (83-MER)
I: Retron Eco8 reverse transcriptase
J: Retron Eco8 OLD nuclease
K: RNA (82-MER)
L: DNA (83-MER)
M: Retron Eco8 reverse transcriptase
N: Retron Eco8 OLD nuclease
O: RNA (82-MER)
P: DNA (83-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,25824
Polymers730,13216
Non-polymers2,1268
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

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Protein , 2 types, 8 molecules AEIMBFJN

#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

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RNA chain / DNA chain , 2 types, 8 molecules CGKODHLP

#3: RNA chain
RNA (82-MER)


Mass: 26291.566 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
#4: DNA chain
DNA (83-MER)


Mass: 25594.412 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)

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Non-polymers , 2 types, 8 molecules

#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Details

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: Retron-Eco8 complex with ATP-Mg2+ / Type: COMPLEX / Entity ID: #1-#4 / 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: 50 e/Å2 / Film or detector model: FEI FALCON IV (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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123608 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00688883
ELECTRON MICROSCOPYf_angle_d0.735160650
ELECTRON MICROSCOPYf_dihedral_angle_d14.46235376
ELECTRON MICROSCOPYf_chiral_restr0.0617546
ELECTRON MICROSCOPYf_plane_restr0.00411341

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