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- PDB-6gzr: Solution NMR structure of the tetramethylrhodamine (TMR) aptamer ... -

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Basic information

Entry
Database: PDB / ID: 6gzr
TitleSolution NMR structure of the tetramethylrhodamine (TMR) aptamer 3 in complex with 5-TAMRA
Componentstetramethylrhodamine aptamer
KeywordsRNA / RNA Aptamer / RNA-Ligand complex / three-way junction
Function / homology5-carboxy methylrhodamine / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDuchardt-Ferner, E. / Ohlenschlager, O. / Kreutz, C.R. / Wohnert, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 902 Germany
Citation
Journal: Nucleic Acids Res. / Year: 2020
Title: Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.
Authors: Duchardt-Ferner, E. / Juen, M. / Bourgeois, B. / Madl, T. / Kreutz, C. / Ohlenschlager, O. / Wohnert, J.
#1: Journal: Biomol NMR Assign / Year: 2017
Title: NMR resonance assignments for the tetramethylrhodamine binding RNA aptamer 3 in complex with the ligand 5-carboxy-tetramethylrhodamine.
Authors: Duchardt-Ferner, E. / Juen, M. / Kreutz, C. / Wohnert, J.
History
DepositionJul 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tetramethylrhodamine aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9262
Polymers15,4941
Non-polymers4311
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: Fluorescence spectroscopy NMR titrations
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8400 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: RNA chain tetramethylrhodamine aptamer


Mass: 15494.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: aptamer from SELEX / Source: (gene. exp.) synthetic construct (others)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical ChemComp-FH8 / 5-carboxy methylrhodamine


Mass: 431.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23N2O5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic3NOESY
222isotropic33D 1H-13C NOESY aromatic
232isotropic33D 1H-13C NOESY aliphatic
2139isotropic23D f1-13C,15N filtered 1H,13C NOESYHSQC
248isotropic23D f1-13C,15N filtered 1H,13C NOESYHSQC
256isotropic23D 1H-13C NOESY aliphatic
295isotropic23D 1H-13C NOESY aromatic
287isotropic33D 1H-13C NOESY aliphatic
272isotropic1f1,f2 filtered NOESY
2103isotropic2HNN-COSY
2113isotropic2SELLR HNN-COSY
2123isotropic2Amino HNN-COSY
1143isotropic215N-1H CPMG-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.2 mM unlabeled TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 95% H2O/5% D2Ounlabeled_sample95% H2O/5% D2O
solution21.2 mM [U-13C; U-15N] TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 95% H2O/5% D2O13C-15N_sample_H2O95% H2O/5% D2O
solution31.2 mM [U-15N] TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution41.2 mM [U-13C; U-15N]-Ade,Cyt TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 95% H2O/5% D2OA,C-13C-15N_sample_H2O95% H2O/5% D2O
solution51.2 mM [U-13C; U-15N]-Gua,Ura TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 95% H2O/5% D2OG,U-13C-15N_sample_H2O95% H2O/5% D2O
solution61.2 mM [U-13C; U-15N]-Ade,Cyt TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 100% D2OA,C-13C-15N_sample_D2O100% D2O
solution71.2 mM [U-13C; U-15N]-Gua,Ura TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 100% D2OG,U-13C-15N_sample_D2O100% D2O
solution81.2 mM [U-13C; U-15N]-Ade TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 95% H2O/5% D2OA-13C-15N-sample_H2O95% H2O/5% D2O
solution91.2 mM [U-13C; U-15N] TMR3_48nt, 1.4 mM unlabeled 5-TAMRA, 100% D2O13C-15N_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMTMR3_48ntunlabeled1
1.4 mM5-TAMRAunlabeled1
1.2 mMTMR3_48nt[U-13C; U-15N]2
1.4 mM5-TAMRAunlabeled2
1.2 mMTMR3_48nt[U-15N]3
1.4 mM5-TAMRAunlabeled3
1.2 mMTMR3_48nt[U-13C; U-15N]-Ade,Cyt4
1.4 mM5-TAMRAunlabeled4
1.2 mMTMR3_48nt[U-13C; U-15N]-Gua,Ura5
1.4 mM5-TAMRAunlabeled5
1.2 mMTMR3_48nt[U-13C; U-15N]-Ade,Cyt6
1.4 mM5-TAMRAunlabeled6
1.2 mMTMR3_48nt[U-13C; U-15N]-Gua,Ura7
1.4 mM5-TAMRAunlabeled7
1.2 mMTMR3_48nt[U-13C; U-15N]-Ade8
1.4 mM5-TAMRAunlabeled8
1.2 mMTMR3_48nt[U-13C; U-15N]9
1.4 mM5-TAMRAunlabeled9
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1130 mM K-Glutamate, 15 mM mMGlutamate buffer 283K7.5 1 bar283 K
2130 mM K-Glutamate, 15 mM NaCl mMGlutamate buffer 298 K7.5 1 bar298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Cryogenic H,C,N triple resonance probe
Bruker AVANCEBrukerAVANCE9002Cryogenic H,C,N triple resonance probe
Bruker AVANCEBrukerAVANCE9503Cryogenic H,C,N triple resonance probe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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