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- PDB-7pdu: Pre-catalytic complex of 10-23 DNAzyme with RNA target -

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Basic information

Entry
Database: PDB / ID: 7pdu
TitlePre-catalytic complex of 10-23 DNAzyme with RNA target
Components
  • 10-23 DNAzyme (33-MER)
  • RNA target (19-MER)
KeywordsDNA-RNA HYBRID / 10-23 DNAzyme / RNA-cleaving DNAzyme / pre-catalytic complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsEtzkorn, M. / Borggrafe, J. / Viegas, A.
Funding supportEuropean Union, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)ET 103/2-1European Union
German Research Foundation (DFG)ET 103/2-2European Union
German Research Foundation (DFG)ET 103/4-1European Union
German Research Foundation (DFG)ET 103/5-1European Union
H2020 Marie Curie Actions of the European CommissionN 660258European Union
CitationJournal: Nature / Year: 2022
Title: Time-resolved structural analysis of an RNA-cleaving DNA catalyst.
Authors: Borggrafe, J. / Victor, J. / Rosenbach, H. / Viegas, A. / Gertzen, C.G.W. / Wuebben, C. / Kovacs, H. / Gopalswamy, M. / Riesner, D. / Steger, G. / Schiemann, O. / Gohlke, H. / Span, I. / Etzkorn, M.
History
DepositionAug 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 10-23 DNAzyme (33-MER)
B: RNA target (19-MER)


Theoretical massNumber of molelcules
Total (without water)16,2472
Polymers16,2472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, Characteristic band for Dz:RNA in native PAGE, NMR Distance Restraints, Characteristic imino peaks visible only after hybridization
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 10-23 DNAzyme (33-MER)


Mass: 10266.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA target (19-MER)


Mass: 5980.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Part of human PrP mRNA / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
133isotropic22D 1H-13C HSQC aliphatic
143isotropic32D 1H-13C HSQC-TOCSY
153isotropic23D 1H-13C NOESY aliphatic
162anisotropic32D 1H-1H NOESY
172isotropic32D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM 110-23 DNAzyme (33-MER), 500 uM RNA target (19-MER), 50 mM n.a. Tris-d11, 100 mM n.a. NaCl, 1 mM n.a. MgCl2, 90% H2O/10% D2O10-23 DNAzyme:RNA complex, RNA target stabilized by 2'F substitution at cleavage siteDz:RNA2'F90% H2O/10% D2O
solution3500 uM [U-13C; U-15N] 110-23 DNAzyme (33-MER), 500 uM RNA target (19-MER), 50 mM n.a. Tris-d11, 100 mM n.a. NaCl, 1 mM n.a. MgCl2, 90% H2O/10% D2O10-23 DNAzyme:RNA complex, RNA target stabilized by 2'F substitution at cleavage site, Dz 13C,15N-enriched13C15N_Dz:RNA2'F90% H2O/10% D2O
solution2750 uM 110-23 DNAzyme (33-MER), 750 uM RNA target (19-MER), 50 mM n.a. Tris-d11, 100 mM n.a. NaCl, 1 mM n.a. MgCl2, 90% H2O/10% D2O10-23 DNAzyme:RNA complex, RNA target stabilized by 2'F substitution at cleavage site. Six addition fluorinations in Dz sequence6xF-Dz:RNA2'F90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uM110-23 DNAzyme (33-MER)none1
500 uMRNA target (19-MER)none1
50 mMTris-d11n.a.1
100 mMNaCln.a.1
1 mMMgCl2n.a.1
500 uM110-23 DNAzyme (33-MER)[U-13C; U-15N]3
500 uMRNA target (19-MER)none3
50 mMTris-d11n.a.3
100 mMNaCln.a.3
1 mMMgCl2n.a.3
750 uM110-23 DNAzyme (33-MER)none2
750 uMRNA target (19-MER)none2
50 mMTris-d11n.a.2
100 mMNaCln.a.2
1 mMMgCl2n.a.2
Sample conditionsIonic strength: 133 mM / Label: Tris_buffer / pH: 7.5 / Pressure: 1 atm / Temperature: 310.12 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9001
Bruker AVANCE III HDBrukerAVANCE III HD7502
Bruker AVANCE III HDBrukerAVANCE III HD6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.0.6Bruker Biospincollection
CARA1.9.1.5Keller and Wuthrichchemical shift assignment
CARA1.9.1.5Keller and Wuthrichpeak picking
Sparky3.114Goddardpeak picking
X-PLOR NIH2.49Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 7

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