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- PDB-1oq0: P6.1 stem loop from the activation domain of hTR -

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Basic information

Entry
Database: PDB / ID: 1oq0
TitleP6.1 stem loop from the activation domain of hTR
ComponentsP6.1 RNA hairpin from hTR
KeywordsRNA / ribonucleoprotein / RNA structure / telomerase / telomeres
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Torsion angle molecular dynamics with simulated anealing in CNS version 5
AuthorsLeeper, T. / Leulliot, N. / Varani, G.
CitationJournal: NUCLEIC ACIDS RES. / Year: 2003
Title: The solution structure of an essential stem-loop of human telomerase RNA
Authors: Leeper, T. / Leulliot, N. / Varani, G.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: P6.1 RNA hairpin from hTR


Theoretical massNumber of molelcules
Total (without water)4,8251
Polymers4,8251
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain P6.1 RNA hairpin from hTR


Mass: 4824.897 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcribed RNA from T7 RNA polymerase and 13C and 15N NTPs or unlabeled NTPs

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
141DQF-COSY
151(H)CCH-COSY
2622D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM RNA, 10 mM Sodium Phosphate, D20D20
20.8 mM RNA, 10 mM Sodium Phosphate, 95% H20, 5% D2095% H20, 5% D20
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
110 mM Na 6300 K
210 mM Na 6277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX7502
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionClassification
CNS5structure solution
XwinNMR3.Xcollection
NMRPipeprocessing
Sparky3.91data analysis
CNS5refinement
RefinementMethod: Torsion angle molecular dynamics with simulated anealing in CNS version 5
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: 20

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