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- PDB-2oj8: NMR structure of the UGUU tetraloop of Duck Epsilon apical stem l... -

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Entry
Database: PDB / ID: 2oj8
TitleNMR structure of the UGUU tetraloop of Duck Epsilon apical stem loop of the Hepatitis B virus
Components5'-R(P*GP*CP*UP*GP*UP*UP*GP*U)-3'
KeywordsRNA / HBV / epsilon / Duck / UGUU / tetraloop
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / Torsion angle dynamics with chemical shift refinement using XPLOR 8.351 with home written refinement chemical shift refinement module
AuthorsGirard, F.C. / Ottink, O.M. / Ampt, K.A.M. / Tessari, M. / Wijmenga, S.S.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals.
Authors: Girard, F.C. / Ottink, O.M. / Ampt, K.A. / Tessari, M. / Wijmenga, S.S.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,5211
Polymers2,5211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 2520.505 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The Sequence of this RNA can be found in Duck Hepatitis B virus

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
132HMQC-15N/1H
343DQF-COSY
354HMQC-13C/1H
3632D NOESY
NMR detailsText: In addition TOCSY spectra and 31P 1D and 31P HMBC spectra were recorded

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Sample preparation

Details
Solution-IDContents
11.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O
21.0 mM 13C/15N/2H-U labeled RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O
31.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O
41.0 mM 13C/15N/2H-U labeled RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM 6.7ambient 5 K
210mM 6.7ambient 15 K
310mM 6.7ambient 25 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 INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR softwareName: X-PLOR / Version: 3.851*
Developer: Girard, F.C., Ottink O.M., Ampt, K.A.M., Tessari, M., Wijmenga, S.S.
Classification: refinement
RefinementMethod: Torsion angle dynamics with chemical shift refinement using XPLOR 8.351 with home written refinement chemical shift refinement module
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: 10

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