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- EMDB-73611: 10-23 DNAzyme in complex with T7 RNA Polymerase -

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Basic information

Entry
Database: EMDB / ID: EMD-73611
Title10-23 DNAzyme in complex with T7 RNA Polymerase
Map dataMap of T7 RNA polymerase in complex with T7 promoter sequence fused to the 10-23 DNAzyme.
Sample
  • Complex: 10-23 DNAzyme in complex with T7 RNA Polymerase
    • Complex: T7 RNA Polymerase
      • Protein or peptide: RNA polymerase
    • Complex: 10-23 DNAzyme
      • DNA: DNA (44-MER)
      • Other: DNA/RNA (5'-D(P*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*AP*GP*AP*AP*T)-R(P*A)-D(P*TP*TP*T)-3')
Keywords10-23 DNAzyme / RNA cleavage / T7 RNA Polymerase / Scaffold / DNA
Function / homology
Function and homology information


DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / DNA-templated transcription / DNA binding
Similarity search - Function
DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesEscherichia phage T7 (virus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.62 Å
AuthorsCramer ER / Shultz HL / Robart AR / Purdy MD / Cooper DR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM133857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM153899 United States
CitationJournal: ACS Chem Biol / Year: 2026
Title: Mapping the Structure and Conformational Landscape of the 10-23 DNAzyme.
Authors: Evan R Cramer / Holly L Shultz / Michael D Purdy / David R Cooper / Aaron R Robart /
Abstract: Deoxyribozymes (DNAzymes) are programmable DNA catalysts with therapeutic and diagnostic potential. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme shown to function using common bioavailable ...Deoxyribozymes (DNAzymes) are programmable DNA catalysts with therapeutic and diagnostic potential. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme shown to function using common bioavailable metal ion cofactors, establishing the potential for DNA-based RNA knockdown . Despite extensive biochemical characterization, structural knowledge on the 10-23 DNAzyme is limited, hindering efforts to rationally improve its activity for physiological applications. To address this need, we developed a T7 RNA polymerase-based protein scaffold that enables cryo-EM visualization of the 10-23 DNAzyme. Using this approach, we obtained a 4.5 Å reconstruction of the DNAzyme-substrate complex and used dimethyl sulfate (DMS) labeling to further examine DNAzyme dynamics. Our structural work supports a model in which the palindromic core folds into a pseudoknot stabilized by guanine stacking, creating a rigid element that organizes subsequent folding of the catalytic core and active site. DMS probing further indicates that magnesium binding collapses a flexible A9-A15 loop onto the pseudoknot, compacting the catalytic core. Together, these findings provide insight into 10-23 DNAzyme dynamics through a proposed metal-dependent hinged activation mechanism. The protein scaffolding approach may also serve as a broadly applicable framework for further structural investigations of DNAzymes.
History
DepositionOct 27, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73611.png

Downloads & links

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Map

FileDownload / File: emd_73611.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of T7 RNA polymerase in complex with T7 promoter sequence fused to the 10-23 DNAzyme.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0664
Minimum - Maximum-0.080286145 - 0.43170846
Average (Standard dev.)0.000046392397 (±0.0097122425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_73611_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_73611_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 10-23 DNAzyme in complex with T7 RNA Polymerase

EntireName: 10-23 DNAzyme in complex with T7 RNA Polymerase
Components
  • Complex: 10-23 DNAzyme in complex with T7 RNA Polymerase
    • Complex: T7 RNA Polymerase
      • Protein or peptide: RNA polymerase
    • Complex: 10-23 DNAzyme
      • DNA: DNA (44-MER)
      • Other: DNA/RNA (5'-D(P*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*AP*GP*AP*AP*T)-R(P*A)-D(P*TP*TP*T)-3')

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Supramolecule #1: 10-23 DNAzyme in complex with T7 RNA Polymerase

SupramoleculeName: 10-23 DNAzyme in complex with T7 RNA Polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 120 KDa

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Supramolecule #2: T7 RNA Polymerase

SupramoleculeName: T7 RNA Polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia phage T7 (virus)

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Supramolecule #3: 10-23 DNAzyme

SupramoleculeName: 10-23 DNAzyme / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: RNA polymerase

MacromoleculeName: RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 99.813117 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNTINIAKND FSDIELAAIP FNTLADHYGE RLAREQLALE HESYEMGEAR FRKMFERQLK AGEVADNAAA KPLITTLLPK MIARINDWF EEVKAKRGKR PTAFQFLQEI KPEAVAYITI KTTLACLTSA DNTTVQAVAS AIGRAIEDEA RFGRIRDLEA K HFKKNVEE ...String:
MNTINIAKND FSDIELAAIP FNTLADHYGE RLAREQLALE HESYEMGEAR FRKMFERQLK AGEVADNAAA KPLITTLLPK MIARINDWF EEVKAKRGKR PTAFQFLQEI KPEAVAYITI KTTLACLTSA DNTTVQAVAS AIGRAIEDEA RFGRIRDLEA K HFKKNVEE QLNKRVGHVY KKAFMQVVEA DMLSKGLLGG EAWSSWHKED SIHVGVRCIE MLIESTGMVS LHRQNAGVVG QD SETIELA PEYAEAIATR AGALAGISPM FQPCVVPPKP WTGITGGGYW ANGRRPLALV RTHSKKALMR YEDVYMPEVY KAI NIAQNT AWKINKKVLA VANVITKWKH CPVEDIPAIE REELPMKPED IDMNPEALTA WKRAAAAVYR KDKARKSRRI SLEF MLEQA NKFANHKAIW FPYNMDWRGR VYAVSMFNPQ GNDMTKGLLT LAKGKPIGKE GYYWLKIHGA NCAGVDKVPF PERIK FIEE NHENIMACAK SPLENTWWAE QDSPFCFLAF CFEYAGVQHH GLSYNCSLPL AFDGSCSGIQ HFSAMLRDEV GGRAVN LLP SETVQDIYGI VAKKVNEILQ ADAINGTDNE VVTVTDENTG EISEKVKLGT KALAGQWLAY GVTRSVTKRS VMTLAYG SK EFGFRQQVLE DTIQPAIDSG KGLMFTQPNQ AAGYMAKLIW ESVSVTVVAA VEAMNWLKSA AKLLAAEVKD KKTGEILR K RCAVHWVTPD GFPVWQEYKK PIQTRLNLMF LGQFRLQPTI NTNKDSEIDA HKQESGIAPN FVHSQDGSHL RKTVVWAHE KYGIESFALI HDSFGTIPAD AANLFKAVRE TMVDTYESCD VLADFYDQFA DQLHESQLDK MPALPAKGNL NLRDILESDF AFAHHHHHH

UniProtKB: T7 RNA polymerase

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Macromolecule #2: DNA (44-MER)

MacromoleculeName: DNA (44-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.533743 KDa
SequenceString:
(DT)(DG)(DG)(DC)(DG)(DA)(DA)(DA)(DG)(DG) (DC)(DT)(DA)(DG)(DC)(DT)(DA)(DC)(DA)(DA) (DC)(DG)(DA)(DA)(DT)(DT)(DC)(DT)(DA) (DA)(DT)(DA)(DC)(DG)(DA)(DC)(DT)(DC)(DA) (DC) (DT)(DA)(DT)(DA)

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Macromolecule #3: DNA/RNA (5'-D(P*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*AP*GP*A...

MacromoleculeName: DNA/RNA (5'-D(P*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*AP*GP*AP*AP*T)-R(P*A)-D(P*TP*TP*T)-3')
type: other / ID: 3 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.728906 KDa
SequenceString:
(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DG) (DT)(DG)(DA)(DG)(DT)(DC)(DG)(DT)(DA)(DT) (DT)(DA)(DG)(DA)(DA)(DT)A(DT)(DT) (DT)(DC)(DG)(DC)(DC)(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

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
30.0 mMMgCl2Magnesium Chloride
20.0 mMTris(hydroxymethyl)aminomethane
150.0 mMNaClSodium Chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.3.1) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1cez


Details: Crystal structure of T7RNA Polymerase in complex with T7 promoter
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.3.1) / Number images used: 10059
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. v4.3.1) / Details: Ab initio reconstruction
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. v4.3.1) / Details: Ab initio reconstruction
Final 3D classificationNumber classes: 1 / Avg.num./class: 10000 / Software - Name: cryoSPARC (ver. v4.3.1)

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