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- PDB-1z31: The structure of an enzyme-activating fragment of human telomerase RNA -

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Basic information

Entry
Database: PDB / ID: 1z31
TitleThe structure of an enzyme-activating fragment of human telomerase RNA
Componentshuman telomerase PJ6 hairpin
KeywordsRNA / asymmetric internal bulge / residual dipolar couplings / telomerase protein binding site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLeeper, T.C. / Varani, G.
CitationJournal: RNA / Year: 2005
Title: The structure of an enzyme-activating fragment of human telomerase RNA.
Authors: Leeper, T.C. / Varani, G.
History
DepositionMar 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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: human telomerase PJ6 hairpin


Theoretical massNumber of molelcules
Total (without water)10,1831
Polymers10,1831
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 the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: RNA chain human telomerase PJ6 hairpin


Mass: 10183.078 Da / Num. of mol.: 1 / Fragment: human telomerase RNA / Source method: obtained synthetically
Details: 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 TOCSY
1212D NOESY
2322D NOESY
1433D 13C-separated NOESY
2543D 13C-separated NOESY
165IPAP-HSQC
173HCP triple resonance
1833D 13C-31P HETCOR
1933D 13C TOCSY-HSQC
2104HNN-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1PJ6 1 mM unlabeled; 10 mM sodium phoshate, pH 6.0, 100% D2O100% D2O
2PJ6 1 mM unlabeled; 10 mM sodium phoshate, pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
3PJ6 0.6 mM U-15N,13C; 10 mM sodium phoshate, pH 6.0, 100% D2O100% D2O
4PJ6 0.6 mM U-15N,13C; 10 mM sodium phoshate, pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
5PJ6 0.6 mM U-15N,13C; 10 mM sodium succinate, pH 6.0, 18 mg/ml Pf1 bacteriaphage, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM 61 atm298 K
210 mM 61 atm277 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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3collection
NMRPipe2.3Delaglioprocessing
X-PLOR2.9.4Brunger and Clorestructure solution
Sparky3.11Goddard and Knellerdata analysis
X-PLOR2.9.4Brunger and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 726 total restraints, 429 NOE-derived restraints, 159 dihedral restraints, 65 residual dipolar coupling restraints, 62 hydrogen bonds, and 11 weak planarity restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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