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- PDB-1z30: NMR structure of the apical part of stemloop D from cloverleaf 1 ... -

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Entry
Database: PDB / ID: 1z30
TitleNMR structure of the apical part of stemloop D from cloverleaf 1 of bovine enterovirus 1 RNA
Components5'-R(*GP*GP*CP*GP*UP*UP*CP*GP*UP*UP*AP*GP*AP*AP*CP*GP*UP*C)-3'
KeywordsRNA / cGUUAg RNA tetraloop / cUNCGg-type backbone conformation / A-form helix
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, energy minimisation
AuthorsIhle, Y. / Ohlenschlager, O. / Duchardt, E. / Ramachandran, R. / Gorlach, M.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA
Authors: Ihle, Y. / Ohlenschlager, O. / Hafner, S. / Duchardt, E. / Zacharias, M. / Seitz, S. / Zell, R. / Ramachandran, R. / Gorlach, M.
History
DepositionMar 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,7651
Polymers5,7651
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)15 / 100structures with the lowest energy, target function
RepresentativeModel #5closest to the average

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Components

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


Mass: 5765.451 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence of this RNA naturally exist in bovine enterovirus 1 (Virus)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM U-[15N]-BEVSLDap RNA90% H2O/10% D2O
20.9mM U-[13C,15N]-BEVSLDap RNA90% H2O/10% D2O
30.9mM U-[13C,15N]-BEVSLDap RNA99.99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA 6.2 ambient 298 K
210mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA 6.2 ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1, rev. cVarian Inc.collection
VNMR6.1, rev. cVarian Inc.processing
XEASY1.3.9Bartelsdata analysis
CYANA1.0.6Herrmannstructure solution
FOUNDimplemented in CYANA-1.0.6Guntertstructure solution
OPAL2.6Luginbuhlrefinement
RefinementMethod: distance geometry, simulated annealing, energy minimisation
Software ordinal: 1
Details: 518 upper limit distance constraints derived from NOE cross peaks, 184 torsion angle constraints defining 156 torsion angles, 36 hydrogen bond constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 15

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