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- PDB-2evy: GNYA tetranucleotide loops found in poliovirus oriL by in vivo SE... -

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Basic information

Entry
Database: PDB / ID: 2evy
TitleGNYA tetranucleotide loops found in poliovirus oriL by in vivo SELEX (un)expectedly form a YNMG-like structure
ComponentsPoliovirus 5'NTR cloverleaf stem loop D mutant
KeywordsRNA / Poliovirus / 5'NTR / cloverleaf / GNYA tetranucleoitde loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMelchers, W.J.G. / Zoll, J. / Tessari, M. / Bakhmutov, D.V. / Gmyl, A.P. / Agol, V.I. / Heus, H.A.
CitationJournal: RNA / Year: 2006
Title: A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA.
Authors: Melchers, W.J.G. / Zoll, J. / Tessari, M. / Bakhmutov, D.V. / Gmyl, A.P. / Agol, V.I. / Heus, H.A.
History
DepositionNov 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: 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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poliovirus 5'NTR cloverleaf stem loop D mutant


Theoretical massNumber of molelcules
Total (without water)4,4641
Polymers4,4641
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)18 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain Poliovirus 5'NTR cloverleaf stem loop D mutant


Mass: 4463.691 Da / Num. of mol.: 1 / Fragment: Poliovirus 5'NTR cloverleaf stem loop D / Mutation: U6G, U7C, C8U, G9A / Source method: obtained synthetically / Details: This sequence naturally occurs in the Polio virus

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
142DQF-COSY
15213C, 1H HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM oligonucleotide;90% H2O/10% D2O
21 mM oligonucleotide100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 mM 6.2ambient 300 K
25 mM 6.2ambient 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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1F. Delaglioprocessing
Sparky3.106T.D. Goddard, D.G. Knellerdata analysis
X-PLORX-PLOR NIHA.T. Brungerstructure solution
X-PLORX-PLOR NIHA.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: 18

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