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- PDB-6k84: Structure of anti-prion RNA aptamer -

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Basic information

Entry
Database: PDB / ID: 6k84
TitleStructure of anti-prion RNA aptamer
ComponentsRNA (25-MER)
KeywordsRNA / Quadruplex / Aptamer
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsMashima, T. / Lee, J.H. / Hayashi, T. / Nagata, T. / Kinoshita, M. / Katahira, M.
CitationJournal: Sci Rep / Year: 2020
Title: Development and structural determination of an anti-PrPCaptamer that blocks pathological conformational conversion of prion protein.
Authors: Mashima, T. / Lee, J.H. / Kamatari, Y.O. / Hayashi, T. / Nagata, T. / Nishikawa, F. / Nishikawa, S. / Kinoshita, M. / Kuwata, K. / Katahira, M.
History
DepositionJun 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 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:
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Assembly

Deposited unit
A: RNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)8,4411
Polymers8,4411
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3620 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (25-MER)


Mass: 8441.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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
111isotropic22D 1H-1H NOESY
221isotropic12D JR-HMBC
232isotropic12D 1H-1H NOESY
242isotropic12D DQF-COSY
252isotropic12D 1H-1H TOCSY
262isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 95% H2O/5% D2OH2O_sample95% H2O/5% D2O
solution21.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRNA (25-MER)natural abundance1
10 mMpotassium phosphatenatural abundance1
10 mMpotassium chloridenatural abundance1
10 uMDSSnatural abundance1
1.0 mMRNA (25-MER)natural abundance2
10 mMpotassium phosphatenatural abundance2
10 mMpotassium chloridenatural abundance2
10 uMDSSnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mMconditions_16.2 1 atm278 K
210 mMconditions_26.2 1 atm288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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