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- PDB-2fey: The structure of stem loop IV of Tetrahymena telomerase RNA -

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Entry
Database: PDB / ID: 2fey
TitleThe structure of stem loop IV of Tetrahymena telomerase RNA
Componentsstem-loop IV of Tetrahymena telomerase RNA
KeywordsRNA / telomerase RNA / Tetrahymena / stem-loop IV / heptaloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, simulated annealing
AuthorsChen, Y. / Fender, J. / Legassie, J.D. / Jarstfer, M.B. / Bryan, T.M. / Varani, G.
CitationJournal: Embo J. / Year: 2006
Title: Structure of stem-loop IV of Tetrahymena telomerase RNA.
Authors: Chen, Y. / Fender, J. / Legassie, J.D. / Jarstfer, M.B. / Bryan, T.M. / Varani, G.
History
DepositionDec 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 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: 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 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: stem-loop IV of Tetrahymena telomerase RNA


Theoretical massNumber of molelcules
Total (without water)13,6851
Polymers13,6851
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 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: RNA chain stem-loop IV of Tetrahymena telomerase RNA


Mass: 13685.097 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence naturally occurs in the stem-loop IV of Tetrahymena telomerase RNA. It was synthesized by T7 RNA Polymerase in vitro transcription from DNA oligonucleotide template.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1333D 13C-separated NOESY
143HCP TRIPLE RESONANCE
1533D 13C-31P HETCOR
1633D 13C TOCSY-HSQC
174HNN-COSY
185IPAP-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 MM unlabelled samples10 mM SODIUM PHOSHATE, PH 6.0, 100% D2O
21 MM unlabelled samples10 mM SODIUM PHOSHATE, PH 6.0, 90% H2O, 10% D2O
30.5 mM, 15N,13C-labelled10 mM SODIUM PHOSHATE, PH 6.0, 100% D2O
40.5 mM, 15N,13C-labelled10 mM SODIUM PHOSHATE, PH 6.0, 90% H2O, 10% D2O
50.5 mM, 15N,13C-labelled10 MM SODIUM SUCCINATE, PH 6.0, 14 MG/ML PF1 BACTERIAPHAGE, 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM 61 atm298 K
210mM 61 atm278 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
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR2.9.7Clore, G.M. & Kuszewski, J.structure solution
NMRPipe2.3F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
Sparky3.11T. D. Goddard and D. G. Knellerdata analysis
XwinNMR3Brukercollection
X-PLOR2.9.7Clore, G.M. & Kuszewski, J.refinement
RefinementMethod: TORSION ANGLE DYNAMICS, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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