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- PDB-1ik1: Solution Structure of an RNA Hairpin from HRV-14 -

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Basic information

Entry
Database: PDB / ID: 1ik1
TitleSolution Structure of an RNA Hairpin from HRV-14
Components5'-R(*GP*GP*UP*AP*CP*UP*AP*UP*GP*UP*AP*CP*CP*A)-3'
KeywordsRNA / A form helix / triloop
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsHuang, H. / Alexandrov, A. / Chen, X. / Barnes III, T.W. / Zhang, H. / Dutta, K. / Pascal, S.M.
CitationJournal: Biochemistry / Year: 2001
Title: Structure of an RNA hairpin from HRV-14.
Authors: Huang, H. / Alexandrov, A. / Chen, X. / Barnes III, T.W. / Zhang, H. / Dutta, K. / Pascal, S.M.
History
DepositionMay 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4481
Polymers4,4481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

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


Mass: 4447.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRV-14 stem loop d hairpin / References: GenBank: 9626735

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
1411H,31P-HETCOR
1511H,13C-HMQC
2622D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM RNA 14mer; 10 mM NaPi, 90 mM NaCl, 0.1 mM EDTA, pH 7.0100% D2O
20.5 mM RNA 14mer; 10 mM NaPi, 90 mM NaCl, 0.1 mM EDTA, pH 7.090% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM 7.0 ambient 298 K
2100 mM 7.0 ambient 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameClassification
VNMRcollection
NMRPipeprocessing
NMRDrawdata analysis
NMRViewdata analysis
DISCOVERstructure solution
DISCOVERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: A total of 172 distance restraints and 40 dihedral angle restraints.
NMR ensembleConformers submitted total number: 1

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