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- PDB-2n7x: Solution structure of microRNA 20b pre-element -

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Basic information

Entry
Database: PDB / ID: 2n7x
TitleSolution structure of microRNA 20b pre-element
ComponentsRNA (5'-R(*GP*GP*UP*AP*GP*UP*UP*UP*UP*GP*GP*CP*AP*UP*GP*AP*CP*UP*CP*UP*AP*CP*C)-3')
KeywordsRNA / microRNA / UU base pair / UC mismatch / stem loop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / restrained simulated annealing
AuthorsYang, F. / Chen, Y. / Varani, G.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer.
Authors: Chen, Y. / Zubovic, L. / Yang, F. / Godin, K. / Pavelitz, T. / Castellanos, J. / Macchi, P. / Varani, G.
History
DepositionSep 25, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 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 1.3May 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: RNA (5'-R(*GP*GP*UP*AP*GP*UP*UP*UP*UP*GP*GP*CP*AP*UP*GP*AP*CP*UP*CP*UP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3181
Polymers7,3181
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7318.335 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-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
2322D 1H-1H TOCSY
3432D 1H-13C HSQC
3533D 1H-13C NOESY
4642D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O100% D2O
31 mM [U-99% 13C; U-99% 15N] miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O100% D2O
41 mM [U-99% 13C; U-99% 15N] miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMmiR-20b-11
10 mMsodium phosphate-21
20 mMsodium chloride-31
1 mMmiR-20b-42
10 mMsodium phosphate-52
20 mMsodium chloride-62
1 mMmiR-20b-7[U-99% 13C; U-99% 15N]3
10 mMsodium phosphate-83
20 mMsodium chloride-93
1 mMmiR-20b-10[U-99% 13C; U-99% 15N]4
10 mMsodium phosphate-114
20 mMsodium chloride-124
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5ambient atm279 K
26.5ambient atm298 K
36.5ambient atm298 K
46.5ambient atm279 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
CcpNMRCCPNdata analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: restrained simulated annealing / 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: 20

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