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- PDB-2mnc: oligonucleotide model of miR-21 pre-element -

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Basic information

Entry
Database: PDB / ID: 2mnc
Titleoligonucleotide model of miR-21 pre-element
ComponentsRNA (5'-R(*GP*GP*GP*UP*UP*GP*AP*CP*CP*GP*UP*UP*GP*AP*AP*UP*CP*UP*CP*AP*CP*GP*GP*CP*AP*AP*CP*CP*C)-3')
KeywordsRNA / miR-21 / microRNA / pre-element
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsChirayil, S. / Wu, Q. / Amezcua, C. / Luebke, K.
CitationJournal: Plos One / Year: 2014
Title: NMR Characterization of an Oligonucleotide Model of the MiR-21 Pre-Element.
Authors: Chirayil, S. / Wu, Q. / Amezcua, C. / Luebke, K.J.
History
DepositionApr 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2May 1, 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

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*GP*UP*UP*GP*AP*CP*CP*GP*UP*UP*GP*AP*AP*UP*CP*UP*CP*AP*CP*GP*GP*CP*AP*AP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)9,2761
Polymers9,2761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (5'-R(*GP*GP*GP*UP*UP*GP*AP*CP*CP*GP*UP*UP*GP*AP*AP*UP*CP*UP*CP*AP*CP*GP*GP*CP*AP*AP*CP*CP*C)-3')


Mass: 9275.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: miR-21_pre-element

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC

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Sample preparation

DetailsContents: 1 mM miR-21 pre-element-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: miR-21 pre-element-1
Sample conditionsIonic strength: 10 / pH: 6.7 / Pressure: ambient atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 14

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