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- PDB-2l2j: Solution NMR structure of the lower part of the R/G stem loop RNA -

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Basic information

Entry
Database: PDB / ID: 2l2j
TitleSolution NMR structure of the lower part of the R/G stem loop RNA
ComponentsRNA (42-MER)
KeywordsRNA / STEM-LOOP / RNA-EDITING / AC MISMATCH
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsOberstrass, F.F. / Allain, F.H.-T. / Stefl, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove.
Authors: Stefl, R. / Oberstrass, F.C. / Hood, J.L. / Jourdan, M. / Zimmermann, M. / Skrisovska, L. / Maris, C. / Peng, L. / Hofr, C. / Emeson, R.B. / Allain, F.H.
History
DepositionAug 20, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (42-MER)


Theoretical massNumber of molelcules
Total (without water)13,4701
Polymers13,4701
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (42-MER)


Mass: 13470.015 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-IDType
1112D 1H-1H NOESY
1223D 1H-13C NOESY
1322D 1H-13C HSQC
1412D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM RNA (42-MER)-1, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM RNA (42-MER)-2, 100% D2O100% D2O
31.5 mM RNA (42-MER)-3, 100% D2O100% D2O
41.5 mM RNA (42-MER)-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMRNA (42-MER)-11
1.5 mMRNA (42-MER)-22
1.5 mMRNA (42-MER)-33
1.5 mMRNA (42-MER)-44
Sample conditionsIonic strength: 20 / pH: 6.2 / Pressure: AMBIENT / Temperature: 278 K

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NMR measurement

NMR spectrometerType: BRUKER DRX, AVANCE / Manufacturer: Bruker / Model: DRX, AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AmberCASE, D.A. ET AL.refinement
TopSpin2Bruker Biospinstructure solution
SparkyGoddardstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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