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- PDB-5uzt: Structure of wild type pre-miR21 apical loop -

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Basic information

Entry
Database: PDB / ID: 5uzt
TitleStructure of wild type pre-miR21 apical loop
Componentspre-miR-21
KeywordsRNA / microRNA miR-21 oncomiR pre-miRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsShortridge, M.D. / Varani, G.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing.
Authors: Shortridge, M.D. / Walker, M.J. / Pavelitz, T. / Chen, Y. / Yang, W. / Varani, G.
History
DepositionFeb 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pre-miR-21


Theoretical massNumber of molelcules
Total (without water)9,9131
Polymers9,9131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 125structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain pre-miR-21


Mass: 9912.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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
232isotropic12D 1H-1H TOCSY
262isotropic22D 1H-1H NOESY
223isotropic23D 1H-13C NOESY
144isotropic22D 1H-15N HSQC
154isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.1 mM pre-miR-21, 10 mM potassium phosphate, 10 mM sodium chloride, 0.01 mM EDTA, 95% H2O/5% D2Ostandard nmr buffer for RNA hairpinsExchangeable protons95% H2O/5% D2O
solution21.1 mM pre-miR-21, 10 mM potassium phosphate, 10 mM sodium chloride, 0.01 mM EDTA, 100% D2Ostandard nmr buffer for RNA hairpinsNon-exchangeable protons100% D2O
solution30.5 mM [U-99% 13C; U-99% 15N] pre-miR-21, 10 mM potassium phosphate, 10 mM sodium chloride, 0.01 mM EDTA, 100% D2Ouniformly labeled RNA sampleLabeled RNA100% D2O
solution40.5 mM [U-99% 13C; U-99% 15N] pre-miR-21, 10 mM potassium phosphate, 10 mM sodium chloride, 0.01 g/L EDTA, 95% H2O/5% D2Ouniformly labeled RNA sampleLabeled RNA295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMpre-miR-21natural abundance1
10 mMpotassium phosphatenatural abundance1
10 mMsodium chloridenatural abundance1
0.01 mMEDTAnatural abundance1
1.1 mMpre-miR-21natural abundance2
10 mMpotassium phosphatenatural abundance2
10 mMsodium chloridenatural abundance2
0.01 mMEDTAnatural abundance2
0.5 mMpre-miR-21[U-99% 13C; U-99% 15N]3
10 mMpotassium phosphatenatural abundance3
10 mMsodium chloridenatural abundance3
0.01 mMEDTAnatural abundance3
0.5 mMpre-miR-21[U-99% 13C; U-99% 15N]4
10 mMpotassium phosphatenatural abundance4
10 mMsodium chloridenatural abundance4
0.01 g/LEDTAnatural abundance4
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1Sample conditions to identify exchangeable protons and 15N chemical shifts. Low temperatures were used to reduce base-pair breathing and exchange with solvent. The RNA sample was snapped cooled prior to NMR data collection (heated 95C for 4min then at -20C until frozen, sample was thawed on ice prior to data collection)10 mMconditions_16.51 atm278 K
2Sample conditions to identify non-exchangeable protons and 13C chemical shifts. The RNA sample was snapped cooled prior to NMR data collection (heated 95C for 4min then at -20C until frozen, sample was thawed on ice prior to data collection)10 mMconditions_26.51 atm310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
AnalysisCCPNchemical shift assignment
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 125 / Conformers submitted total number: 10

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