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- PDB-2grw: Solution structure of the poliovirus 3'-UTR Y-stem -

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Basic information

Entry
Database: PDB / ID: 2grw
TitleSolution structure of the poliovirus 3'-UTR Y-stem
Components5'-GGACCUCUCGAAAGAGAUGUCC-3'
KeywordsRNA / poliovirus / stem-loop / pseudo-2-fold symmetry
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHeus, H.A. / Zoll, J. / Tessari, M. / van Kuppeveld, F.J.M. / Melchers, W.J.G.
CitationJournal: Rna / Year: 2007
Title: Breaking pseudo-twofold symmetry in the poliovirus 3'-UTR Y-stem by restoring Watson-Crick base pairs.
Authors: Zoll, J. / Tessari, M. / Van Kuppeveld, F.J.M. / Melchers, W.J.G. / Heus, H.A.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: 5'-GGACCUCUCGAAAGAGAUGUCC-3'


Theoretical massNumber of molelcules
Total (without water)7,0571
Polymers7,0571
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)12 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-GGACCUCUCGAAAGAGAUGUCC-3'


Mass: 7057.267 Da / Num. of mol.: 1 / Fragment: poliovirus 3'-UTR Y-stem / Source method: obtained synthetically
Details: This sequence is a mutant of poliovirus 3'-UTR Y-stem

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY
2422D TOCSY
2522D-HSQC
3632D-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM RNA 13C,15N, pH 6.890% H2O/10% D2O
22mM RNA 13C,15N, pH 6.8100% D2O
32mM RNA 13C, 15N, pH 6.8, 27 mg/ml philamentous phage Pf1100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 mM 6.8ambient 300 K
25 mM 6.8ambient 300 K
35 mM 6.8ambient 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipe2.1F. Delaglioprocessing
Sparky3.106T.D. Goddard and D.G. Knellerdata analysis
X-PLOR3.1A.T. Brungerstructure solution
X-PLOR3.1A.T. Brungerrefinement
RefinementMethod: torsion angle dynamics / 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: 12

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