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- PDB-1roq: Extending the Family of UNCG-like Tetraloop Motifs: NMR Structure... -

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Entry
Database: PDB / ID: 1roq
TitleExtending the Family of UNCG-like Tetraloop Motifs: NMR Structure of a CACG Tetraloop from Coxsackievirus B3
Components5'-R(*GP*GP*UP*AP*UP*CP*AP*CP*GP*GP*UP*AP*CP*C)-3'
KeywordsRNA / RNA tetra-loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsDu, Z. / Yu, J. / Andino, R. / James, T.L.
CitationJournal: Biochemistry / Year: 2003
Title: Extending the Family of UNCG-like Tetraloop Motifs: NMR Structure of a CACG Tetraloop from Coxsackievirus B3
Authors: Du, Z. / Yu, J. / Andino, R. / James, T.L.
History
DepositionDec 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 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: 5'-R(*GP*GP*UP*AP*UP*CP*AP*CP*GP*GP*UP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,4631
Polymers4,4631
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)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4462.707 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE, this sequence occurs naturally in Coxsackievirus B3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsContents: 1-2mM RNA, 25mM sodium phosphate (pH 6.0), 25mM sodium chloride
Solvent system: 25mM sodium phosphate (pH 6.0), 25mM sodium chloride
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125 mM NaCl 6ambient 278 K
225 mM NaCl 6ambient 283 K
325 mM NaCl 6ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P.structure solution
CNS1Brunger A.refinement
Sparky1Goddard T.data analysis
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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