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- EMDB-66366: Cryo-EM structure of the hexameric DRT6 -

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Basic information

Entry
Database: EMDB / ID: EMD-66366
TitleCryo-EM structure of the hexameric DRT6
Map data
Sample
  • Complex: DRT6
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein
KeywordsUG12 / DRT6 / Reverse transcriptases / UG/Abi system / IMMUNE 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsWang Y / Deng Z
Funding support1 items
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, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66366.png

Downloads & links

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Map

FileDownload / File: emd_66366.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.182
Minimum - Maximum-1.4217124 - 2.2762287
Average (Standard dev.)0.0015169191 (±0.076932386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66366_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_66366_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : DRT6

EntireName: DRT6
Components
  • Complex: DRT6
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein

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Supramolecule #1: DRT6

SupramoleculeName: DRT6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Reverse transcri...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Reverse transcriptase domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 109.366672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSSGL VPRGSHMKIE EGKLVIWING DKGYNGLAEV GKKFEKDTGI KVTVEHPDKL EEKFPQVAAT GDGPDIIFWA HDRFGGYAQ SGLLAEITPD KAFQDKLYPF TWDAVRYNGK LIAYPIAVEA LSLIYNKDLL PNPPKTWEEI PALDKELKAK G KSALMFNL ...String:
HHHHHHSSGL VPRGSHMKIE EGKLVIWING DKGYNGLAEV GKKFEKDTGI KVTVEHPDKL EEKFPQVAAT GDGPDIIFWA HDRFGGYAQ SGLLAEITPD KAFQDKLYPF TWDAVRYNGK LIAYPIAVEA LSLIYNKDLL PNPPKTWEEI PALDKELKAK G KSALMFNL QEPYFTWPLI AADGGYAFKY ENGKYDIKDV GVDNAGAKAG LTFLVDLIKN KHMNADTDYS IAEAAFNKGE TA MTINGPW AWSNIDTSKV NYGVTVLPTF KGQPSKPFVG VLSAGINAAS PNKELAKEFL ENYLLTDEGL EAVNKDKPLG AVA LKSYEE ELAKDPRIAA TMENAQKGEI MPNIPQMSAF WYAVRTAVIN AASGRQTVDE ALKDAQTNSS SGLEVLFQGP GSMD KLKEL LEKGFLPIQL PPGFTSRSYA VKYKKYKPIW ESKKAPSTRA ERFSVARSSY NRRVTSILNP ISYLLLSKEI VKYWP KIQK HYKRSKISLS TPQIFPELRA IKISKFSELY EAKVIRSTGY RYVLITDINR FFPSIYTHTI PWALHTKVIA KKNKEK NAQ YYGNILDNRS MGVQEWQTVG LPIGPDTSHI IAEIIGVAID LQIKDALGKW PSGFRYVDDF YFFFDTRDEA EVALAEL TK AISNFELQIN PSKTRIVEVK SLVEESWKYS LKKLSISYDR RAQRDDIHNY FEALFALESK FFDESLVKYG LKQISSHI I KMSNWDVFEA YLLKCGFSFP NTLQVIVNIL STYNRHGYKL NLSAIERFCN TLVKIHAISD HHGEVSWLLW ICKELGLNL RRDVVREIEG MSSSVCALIT LDLYYSGKIK TNLRVDYLKQ YSNKEALYGS AWLLSYEAGR RGWLKNNNHA YIQNDEFFGP LLKEGVSFY DESMKCSPIF DFKAGALEGI DLNSFFDRDS KIEVHFDFDD MDEEYFDSDH SDDDDDDDDD EDEDEDEDGD I FE

UniProtKB: Maltose/maltodextrin-binding periplasmic protein

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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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 145635
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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