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- PDB-9wy8: Cryo-EM structure of the hexameric DRT6 -

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Basic information

Entry
Database: PDB / ID: 9wy8
TitleCryo-EM structure of the hexameric DRT6
ComponentsMaltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein
KeywordsIMMUNE SYSTEM / UG12 / DRT6 / Reverse transcriptases / UG/Abi system
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsWang, Y. / Deng, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem Biophys Res Commun / Year: 2025
Title: Cryo-EM structure of the bacterial anti-phage defense system DRT6.
Authors: Yong Wang / Hao Wu / Jinyue Li / Zhenhua Tian / Zengqin Deng /
Abstract: Defense-associated reverse transcriptases (DRTs) were recently identified with anti-phage function. Among them, DRT6 represents a single-gene-encoded anti-phage system that confers resistance to ...Defense-associated reverse transcriptases (DRTs) were recently identified with anti-phage function. Among them, DRT6 represents a single-gene-encoded anti-phage system that confers resistance to multiple DNA bacteriophages; however, its structural basis and mechanism of action remain unknown. Here, we determined a high-resolution cryo-EM structure of DRT6, revealing that it assembles into a hexamer composed of two trimers arranged in a back-to-back configuration. Structure-guided mutagenesis demonstrated that the integrity of this hexameric interface is critical for both the stability and anti-phage activity of DRT6. Comparative structural analysis showed that DRT6 shares notable similarity with the anti-phage protein AbiK. Intriguingly, the thumb subdomain of its reverse transcriptase domain is replaced by an α-helical repeat (αRep) domain, forming a positively charged channel that likely mediates nucleic acid binding. Nevertheless, DRT6 differs from AbiK in the position of its priming amino acid, suggesting distinct functional mechanisms. Together, this work reports the first atomic structure of DRT6, elucidates the molecular basis of its functional oligomerization, and provides insights into the anti-phage mechanism.
History
DepositionSep 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein
B: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein
C: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein
D: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein
E: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein
F: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)656,2006
Polymers656,2006
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 109366.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Escherichia coli (E. coli)
Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
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: DRT6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
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

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145635 / Symmetry type: POINT
RefinementHighest resolution: 2.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00525080
ELECTRON MICROSCOPYf_angle_d0.76133888
ELECTRON MICROSCOPYf_dihedral_angle_d5.3033300
ELECTRON MICROSCOPYf_chiral_restr0.0513666
ELECTRON MICROSCOPYf_plane_restr0.0074212

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