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- EMDB-73864: Cryo-EM hexamer map of the elongating EcDRT3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-73864
TitleCryo-EM hexamer map of the elongating EcDRT3 complex
Map data
Sample
  • Complex: Hexameric complex of DRT3-ncRNA
    • Protein or peptide: Drt3a reverse transcriptase protein
    • Protein or peptide: Drt3b reverse transcriptase protein
    • RNA: non-coding RNA
    • DNA: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
    • DNA: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: PYROPHOSPHATE 2-
  • Ligand: water
KeywordsDRT3-ncRNA complex / reverse transcriptase / Anti-phage complex / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsDeng P / Gao A
Funding support United States, 1 items
OrganizationGrant numberCountry
The G. Harold and Leila Y. Mathers FoundationMF-2303-04116 United States
CitationJournal: Science / Year: 2026
Title: Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase.
Authors: Pujuan Deng / Hyunbin Lee / Carlo Armijo / Haoqing Wang / Alex Gao /
Abstract: Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two ...Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo-electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.
History
DepositionNov 14, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73864.png

Downloads & links

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Map

FileDownload / File: emd_73864.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 560 pix.
= 470.904 Å		0.84 Å/pix.
x 560 pix.
= 470.904 Å		0.84 Å/pix.
x 560 pix.
= 470.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8409 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.9827371 - 2.6214278
Average (Standard dev.)0.001386792 (±0.04014704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 470.904 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73864_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73864_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexameric complex of DRT3-ncRNA

EntireName: Hexameric complex of DRT3-ncRNA
Components
  • Complex: Hexameric complex of DRT3-ncRNA
    • Protein or peptide: Drt3a reverse transcriptase protein
    • Protein or peptide: Drt3b reverse transcriptase protein
    • RNA: non-coding RNA
    • DNA: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
    • DNA: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: PYROPHOSPHATE 2-
  • Ligand: water

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Supramolecule #1: Hexameric complex of DRT3-ncRNA

SupramoleculeName: Hexameric complex of DRT3-ncRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Drt3a reverse transcriptase protein

MacromoleculeName: Drt3a reverse transcriptase protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 50.34575 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYDQSFNPRT LSRCFKPEDF QKNRALSLDS VREKTIRAAI ERFNNGFLGY NLRSSVLRGK KVYWADELAD TLVLRKVQSN LSNLYQLKL PSRTMIVDTL NVFLSECSQY KLYRLDIHSF YESFNKDYIF KKIDELERLE MKTKQLLKEF LYSFYLTGGE G IPRGLSIS ...String:
MYDQSFNPRT LSRCFKPEDF QKNRALSLDS VREKTIRAAI ERFNNGFLGY NLRSSVLRGK KVYWADELAD TLVLRKVQSN LSNLYQLKL PSRTMIVDTL NVFLSECSQY KLYRLDIHSF YESFNKDYIF KKIDELERLE MKTKQLLKEF LYSFYLTGGE G IPRGLSIS AYLAELLMHD FDNHLKDDKS VFYYARYVDD IVIVTSGFED SNAFIENVKS ILPPGLSFNE GEKYYISDLI PK SANKKNT HHHHHHESPT KLLTFEYLGY DFSVGDKIEE CNIRGFYRLI EVDLAHAKAN KIKSRIIYSI IDYNKTKDFE LLC ERLKFL STNFSILDSG RVLKRLSGIH YNYPLVDART SRRLAELDLF LRKAVLSSNG KVFFDFHANL NQYKKYRLLK ISFV RGHEK RHFFHYSASK MMRIQRCWKY V

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Macromolecule #2: Drt3b reverse transcriptase protein

MacromoleculeName: Drt3b reverse transcriptase protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 76.426602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKKKEVRVN KKDFNRVLVT ETIPYETPII VSNDGFYNNV VKHQTANDIA KLLTQRVILG ERKKGRYTIP YVFKINKNET EFRRLAFPH PISQIEMRDF YLHFNQVMIN FCSKSDFSIR RPVKVASTYY YKNLLEDKNL YKRGPVDTDK NELLTRHASS Y FGYHGYDR ...String:
MSKKKEVRVN KKDFNRVLVT ETIPYETPII VSNDGFYNNV VKHQTANDIA KLLTQRVILG ERKKGRYTIP YVFKINKNET EFRRLAFPH PISQIEMRDF YLHFNQVMIN FCSKSDFSIR RPVKVASTYY YKNLLEDKNL YKRGPVDTDK NELLTRHASS Y FGYHGYDR LYKFFMSNDF IDLERKYNTL YTLDVSKCFD SIYTHSISWA TKTKTFTKGM LANKSLNFGD AFDKLMQRCN FN ETHGVII GPEISRIFAE IIFQKIDLNV QFKLRNIDTP LNKGVDYDIR RYVDDVFIFS KNEVNAEIIY KVYADKLNEY NMH VNLGKV TKNSRPFITA KTQIIHHVNQ KMNVFIDSFL SYDDEMKLIA KPIYNNRKLA NKFIDEVKII CSERKSGYGE VSSY IVSAI FERIKRLTSS VNQAEDKDIY NVMYVLLHIS LFFFRVAPSV SSSYKLASIL IVTLRYFKAQ VPSYSDLIAS YIYFE IEDF LKAAKNGKKT IDNLVSLEAY NIMYVIGELD QDRYLSKQLV EDVFSEVDSY FDIVSCLYIV KDKKVYDSLK NNIIDV INS KLMSSDNILD YSEKAMLFLD VMSCPYIDLK WKKIWLKSIL KELQEATPNN NEIDSFISYS VANPWFVDWS NVDLLNF LE KKQLKKA(PTR)

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Macromolecule #3: non-coding RNA

MacromoleculeName: non-coding RNA / type: rna / ID: 3 / Number of copies: 6
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 44.236227 KDa
SequenceString:
AAUGCAACCA AUAUGCCCUA CACGAUUUUU CGAUAUACUA GGGCUGAUUA CGGUAGGUAA GUUACACGUA ACCUUAGCUA CCUUAUGAC GCUCAAGAGC AGCAAUGCAC ACACUAAGGG AUGAGGUUGC UUCAAUUUC

GENBANK: GENBANK: CP053259.1

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Macromolecule #4: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')

MacromoleculeName: cDNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*T)-3')
type: dna / ID: 4 / Number of copies: 6 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.326424 KDa
SequenceString:
(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DG) (DT)(DG)(DT)(DG)(DT)(DG)(DT)

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Macromolecule #5: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')

MacromoleculeName: cDNA (5'-D(P*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*AP*CP*A)-3')
type: dna / ID: 5 / Number of copies: 6 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.37654 KDa
SequenceString:
(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 18 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: PYROPHOSPHATE 2-

MacromoleculeName: PYROPHOSPHATE 2- / type: ligand / ID: 7 / Number of copies: 6 / Formula: POP
Molecular weightTheoretical: 175.959 Da
Chemical component information

ChemComp-POP:
PYROPHOSPHATE 2-

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeTFS KRIOS
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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 239792
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9z6y:
Structure of the elongating EcDRT3 reverse transcriptase in complex with its non-coding RNA

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