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- PDB-1na2: Solution structure of the p2b hairpin from human telomerase RNA -

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Basic information

Entry
Database: PDB / ID: 1na2
TitleSolution structure of the p2b hairpin from human telomerase RNA
Componentstelomerase RNA p2b hairpin
KeywordsRNA / U-U base pair / U-C base pair / pentaloop / hairpin / telomerase / narrow minor groove / U tracts
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsTheimer, C.A. / Finger, L.D. / Trantirek, L. / Feigon, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA
Authors: Theimer, C.A. / Finger, L.D. / Trantirek, L. / Feigon, J.
History
DepositionNov 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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: telomerase RNA p2b hairpin


Theoretical massNumber of molelcules
Total (without water)9,4501
Polymers9,4501
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)18 / 200structures 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 telomerase RNA p2b hairpin


Mass: 9449.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (human).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D NOESY
222DQF-COSY
2323D 13C-separated NOESY
2423D 13C NOESY-HMQC
1512D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM human telomerase RNA p2b hairpin U-15N,13C labeled, unlabeled.95% H2O, 5% D2O, 200mM KCl, 0.2% NaN3, 50uM EDTA, 10mM Na phosphate, pH=6.3
21mM human telomerase RNA p2b hairpin U-15N,13C labeled, unlabeled.100% D2O, 200mM KCl, 0.2% NaN3, 50uM EDTA, 10mM Na phosphate, pH=6.3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200 mM KCl 6.31 atm278 K
2200 mM KCl 6.31 atm293 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 DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
AURELIA3.108Brukerdata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 266 intranucleotide NOEs, 318 internucleotide NOEs, 117 dihedral angles, 29 hydrogen bonds, 24 RDCs
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: 200 / Conformers submitted total number: 18

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