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- PDB-2kye: Solution structure of the pseudouridine modified P6.1 hairpin of ... -

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Basic information

Entry
Database: PDB / ID: 2kye
TitleSolution structure of the pseudouridine modified P6.1 hairpin of human telomerase RNA
ComponentsRNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')
KeywordsRNA / telomerase / pseudouridine / P6.1 / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsKim, N.-K. / Theimer, C.A. / Mitchell, J.R. / Collins, K. / Feigon, J.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA.
Authors: Kim, N.K. / Theimer, C.A. / Mitchell, J.R. / Collins, K. / Feigon, J.
History
DepositionMay 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')


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 RNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')


Mass: 4824.897 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
2222D 1H-13C HSQC
2342D 1H-13C HSQC
2442D 1H-1H COSY
1512D 1H-1H NOESY
2622D 1H-1H NOESY
2742D 1H-1H NOESY
2843D (H)CCH-TOCSY
1912D 1H-1H TOCSY
21022D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM RNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')-1, 95% H2O/5% D2O95% H2O/5% D2O
20.6 mM RNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')-2, 100% D2O100% D2O
30.8 mM [U-98% 13C; U-98% 15N] RNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')-3, 95% H2O/5% D2O95% H2O/5% D2O
40.8 mM [U-98% 13C; U-98% 15N] RNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')-11
0.6 mMRNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')-22
0.8 mMRNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')-3[U-98% 13C; U-98% 15N]3
0.8 mMRNA (5'-R(*GP*AP*GP*AP*GP*(PSU)P*(PSU)P*GP*GP*GP*CP*(PSU)P*CP*(PSU)P*C)-3')-4[U-98% 13C; U-98% 15N]4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
156.8ambient 283 K
256.8ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.9.8Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.9.8Schwieters, Kuszewski, Tjandra and Clorerefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
XwinNMRBruker Biospincollection
XwinNMRBruker Biospindata analysis
XwinNMRBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / 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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