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- PDB-9yxm: 10-23 DNAzyme in complex with T7 RNA Polymerase -

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Basic information

Entry
Database: PDB / ID: 9yxm
Title10-23 DNAzyme in complex with T7 RNA Polymerase
Components
  • DNA (44-MER)
  • 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')
  • RNA polymerase
KeywordsDNA / 10-23 DNAzyme / RNA cleavage / T7 RNA Polymerase / Scaffold
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
DNA / DNA (> 10) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / T7 RNA polymerase
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.62 Å
AuthorsCramer, E.R. / Shultz, H.L. / Robart, A.R. / Purdy, M.D. / Cooper, D.R.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase
B: DNA (44-MER)
C: 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')


Theoretical massNumber of molelcules
Total (without water)124,0763
Polymers124,0763
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RNA polymerase / DNA-directed RNA polymerase


Mass: 99813.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T7 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00573, DNA-directed RNA polymerase
#2: DNA chain DNA (44-MER)


Mass: 13533.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA/RNA hybrid 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')


Mass: 10728.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
110-23 DNAzyme in complex with T7 RNA PolymeraseCOMPLEXall0MULTIPLE SOURCES
2T7 RNA PolymeraseCOMPLEX#11RECOMBINANT
310-23 DNAzymeCOMPLEX#2-#31SYNTHETIC
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia phage T7 (virus)10760
33synthetic construct (others)32630
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMMagnesium ChlorideMgCl21
220 mMTris(hydroxymethyl)aminomethane1
3150 mMSodium ChlorideNaCl1
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.3.1particle selection
4cryoSPARCv4.3.1CTF correction
10cryoSPARCv4.3.1initial Euler assignment
11cryoSPARCv4.3.1final Euler assignment
12cryoSPARCv4.3.1classification
13cryoSPARCv4.3.13D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10059 / Num. of class averages: 1 / Symmetry type: POINT

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