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- EMDB-60725: Cryo-EM structure of the hexameric DRT9-ncRNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60725
TitleCryo-EM structure of the hexameric DRT9-ncRNA complex
Map data
Sample
  • Complex: DRT9-ncRNA hexamer complex
    • Protein or peptide: RNA-dependent DNA polymerase
    • RNA: RNA (177-MER)
KeywordsRNA BINDING / PROTEIN-RNA COMPLEX / ANTIVIRAL PROTEIN/RNA / ANTIVIRAL PROTEIN-RNA complex
Function / homology: / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / RNA-dependent DNA polymerase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsZhang JT / Song XY / Xia YS / Liu YJ / Jia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2025
Title: Bacterial reverse transcriptase synthesizes long poly-A-rich cDNA for antiphage defense.
Authors: Xin-Yi Song / Yushan Xia / Jun-Tao Zhang / Yu-Jun Liu / Hua Qi / Xin-Yang Wei / Hailiang Hu / Yu Xia / Xue Liu / Ying-Fei Ma / Ning Jia /
Abstract: Prokaryotic defense-associated reverse transcriptases (DRTs) were recently identified with antiviral functions; however, their functional mechanisms remain largely unexplored. Here we show that DRT9 ...Prokaryotic defense-associated reverse transcriptases (DRTs) were recently identified with antiviral functions; however, their functional mechanisms remain largely unexplored. Here we show that DRT9 forms a hexameric complex with its upstream non-coding RNA (ncRNA) to mediate antiphage defense by inducing cell growth arrest via abortive infection. Upon phage infection, the phage-encoded ribonucleotide reductase NrdAB complex elevates intracellular dATP levels, activating DRT9 to synthesize long, poly-A-rich single-stranded cDNA, which likely sequesters the essential phage SSB protein and disrupts phage propagation. We further determined the cryo-electron microscopy structure of the DRT9-ncRNA hexamer complex, providing mechanistic insights into its cDNA synthesis. These findings highlight the diversity of RT-based antiviral defense mechanisms, expand our understanding of RT biological functions, and provide a structural basis for developing DRT9-based biotechnological tools.
History
DepositionJul 8, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60725.png

Downloads & links

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Map

FileDownload / File: emd_60725.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 438. Å		1.1 Å/pix.
x 400 pix.
= 438. Å		1.1 Å/pix.
x 400 pix.
= 438. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.08106296 - 1.6088266
Average (Standard dev.)0.00040671707 (±0.020866744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 438.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60725_msk_1.map
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Half map: #2

Fileemd_60725_half_map_1.map
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Half map: #1

Fileemd_60725_half_map_2.map
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Sample components

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Entire : DRT9-ncRNA hexamer complex

EntireName: DRT9-ncRNA hexamer complex
Components
  • Complex: DRT9-ncRNA hexamer complex
    • Protein or peptide: RNA-dependent DNA polymerase
    • RNA: RNA (177-MER)

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Supramolecule #1: DRT9-ncRNA hexamer complex

SupramoleculeName: DRT9-ncRNA hexamer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: RNA-dependent DNA polymerase

MacromoleculeName: RNA-dependent DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 58.318961 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKLEQQIQRV ILEEAKALIK DYHEYHNRVH LESVRNKKRL GDSAPDKKIH RPNYWSFDKK FDPFYVKSNY KSIARSIANK IENRTYLPN EPFTKDVPKP DGGIRKVSIY QIPDAAISKL FFNRLLAKNR HRFSSFSYAY RNDRNVHFAI QDISVDLKKN E RTFLAEFD ...String:
MKLEQQIQRV ILEEAKALIK DYHEYHNRVH LESVRNKKRL GDSAPDKKIH RPNYWSFDKK FDPFYVKSNY KSIARSIANK IENRTYLPN EPFTKDVPKP DGGIRKVSIY QIPDAAISKL FFNRLLAKNR HRFSSFSYAY RNDRNVHFAI QDISVDLKKN E RTFLAEFD FSDFFGSISH SFLNEQFNEN GFYISPEEKF IIRSFLRERK VGIPQGTSIS LFLANLTCWK LDQDLEREGV KF SRYADDT IIWSQEYSKI CNAFNIITNF SKSAGIKINP KKSEGISLLT KKGLPSEITS KNNLDFLGYT LSVENVSIKE KSV KKIKKQ ISYILYRNLI QPLKKTSLAG QTIPANDRDK NFLIAICEIR RYMYGGLSKS QIKDYLSGRS NRLYFKGIMS FYPL VNDVE QLKQLDGWIV SVIYRALKLR CQLLSKWGYN RSHNFPFILD REDIVDKCSK KTIAGRKLFE IPSFLLIHKA LQKGL QESG IEKIMNPQSL NYDYE

UniProtKB: RNA-dependent DNA polymerase

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Macromolecule #2: RNA (177-MER)

MacromoleculeName: RNA (177-MER) / type: rna / ID: 2 / Number of copies: 6
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 56.793293 KDa
SequenceString:
AUUCUCUCAU AGGGAUAACG GUGUGGCCUU CUACCUGUUA GAAAUAAUGG GUCUUCAGUU GUAAUUCGUU GCAACUGACG GGGGGGUGG UGUCAAAGCC GUUUCAACCA AGUGGUAACU UACUUUUACU UGGGUUUAUA CCGUGGAAAA GCCUGAGUCU A ACUCAGGC UUUUUUGUU

GENBANK: GENBANK: CP074354.1

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 220612
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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