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- EMDB-65143: Cryo-EM structure of DRT9 tetramer complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65143
TitleCryo-EM structure of DRT9 tetramer complex
Map data
Sample
  • Complex: a protein
    • Protein or peptide: RNA-dependent DNA polymerase
    • RNA: RNA (188-MER)
  • Ligand: MAGNESIUM ION
Keywordsa protein 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: 3.49 Å
AuthorsZhang H / Zhang S
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: EMBO J / Year: 2025
Title: Non-coding RNA mediates the defense-associated reverse transcriptase (DRT) anti-phage oligomerization transition.
Authors: Jie Han / Bin Liu / Jingjing Tang / Shuqin Zhang / Xiaoshen Wang / Xuzichao Li / Qian Zhang / Zhikun Liu / Wanyao Wang / Yingcan Liu / Ruimin Zhou / Hang Yin / Yong Wei / Zhuang Li / Minjie ...Authors: Jie Han / Bin Liu / Jingjing Tang / Shuqin Zhang / Xiaoshen Wang / Xuzichao Li / Qian Zhang / Zhikun Liu / Wanyao Wang / Yingcan Liu / Ruimin Zhou / Hang Yin / Yong Wei / Zhuang Li / Minjie Zhang / Zengqin Deng / Heng Zhang /
Abstract: Defense-associated reverse transcriptase (DRT) systems are implicated in prokaryotic resistance to viral infections, yet the molecular mechanisms underlying their functionality remain largely unknown. ...Defense-associated reverse transcriptase (DRT) systems are implicated in prokaryotic resistance to viral infections, yet the molecular mechanisms underlying their functionality remain largely unknown. Here, we characterize a two-component DRT9 system, composed of a reverse transcriptase (RT) and a non-coding RNA (ncRNA), which exhibits a protein-primed DNA synthesis activity upon phage infection. We also determine its cryo-electron microscopy (cryo-EM) structures in different functional states. DRT9 RT binds to ncRNA, forming a dimer of dimers configuration that assembles into a trimer of dimers upon substrate binding. This oligomerization transition, crucial for DRT9-mediated anti-phage defense, is facilitated by a ncRNA cooperative self-assembly manner. Furthermore, substrate binding induces large conformational movements around the catalytic pocket of DRT9 RT, revealing a "lock-switch" mechanism for enzymatic activation. Notably, phylogenetic analysis and functional assays identify a unique N-terminal helix extension required for ncRNA stabilization and enzymatic activity, distinct from previously reported reverse transcriptase systems. Overall, our findings illuminate the molecular basis of DRT9-mediated antiviral defense and expand the functional and mechanistic diversity of the DRT family.
History
DepositionJun 23, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65143.png

Downloads & links

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Map

FileDownload / File: emd_65143.map.gz / Format: CCP4 / Size: 103 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.)
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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.16004328 - 0.38557673
Average (Standard dev.)0.0021721371 (±0.021053256)
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_65143_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_65143_half_map_2.map
Projections & Slices
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Sample components

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Entire : a protein

EntireName: a protein
Components
  • Complex: a protein
    • Protein or peptide: RNA-dependent DNA polymerase
    • RNA: RNA (188-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: a protein

SupramoleculeName: a protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 58.318961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 (188-MER)

MacromoleculeName: RNA (188-MER) / type: rna / ID: 2 / Number of copies: 4
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 60.361391 KDa
SequenceString:
CAUUCUCUCA UAGGGAUAAC GGUGUGGCCU UCUACCUGUU AGAAAUAAUG GGUCUUCAGU UGUAAUUCGU UGCAACUGAC GGGGGGGUG GUGUCAAAGC CGUUUCAACC AAGUGGUAAC UUACUUUUAC UUGGGUUUAU ACCGUGGAAA AGCCUGAGUC U AACUCAGG CUUUUUUGUU UAGAGGGCUU

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.5
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 correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 210060
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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