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- PDB-2k96: Solution structure of the RDC-refined P2B-P3 pseudoknot from huma... -

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Basic information

Entry
Database: PDB / ID: 2k96
TitleSolution structure of the RDC-refined P2B-P3 pseudoknot from human telomerase RNA (delta U177)
ComponentsTELOMERASE RNA P2B-P3 PSEUDOKNOT
KeywordsRNA / telomerase / Triple helix / RDC
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsA unimolecular pseudoknot construct composed of nucleotides 95-116 and 166-183 with a U177 deletion ...A unimolecular pseudoknot construct composed of nucleotides 95-116 and 166-183 with a U177 deletion (mature hTR RNA numbering system)
AuthorsKim, N.-K. / Zhang, Q. / Zhou, J. / Theimer, C.A. / Peterson, R.D. / Feigon, J.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Solution Structure and Dynamics of the Wild-type Pseudoknot of Human Telomerase RNA.
Authors: Kim, N.K. / Zhang, Q. / Zhou, J. / Theimer, C.A. / Peterson, R.D. / Feigon, J.
#1: Journal: Mol.Cell / Year: 2005
Title: Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function
Authors: Theimer, C.A. / Blois, C.A. / Feigon, J.
History
DepositionSep 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: TELOMERASE RNA P2B-P3 PSEUDOKNOT


Theoretical massNumber of molelcules
Total (without water)14,9831
Polymers14,9831
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain TELOMERASE RNA P2B-P3 PSEUDOKNOT


Mass: 14982.920 Da / Num. of mol.: 1 / Fragment: P2b-P3 pseudoknot / Mutation: U177 deletion / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: A unimolecular pseudoknot construct composed of nucleotides 95-116 and 166-183 with a U177 deletion (mature hTR RNA numbering system)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D JNN-HNN COSY
1212D 1H-15N HSQC
2322D 1H-13C S3CT HSQC
1412D 15N CPMG NOESY
1512D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O95% H2O/5% D2O
21 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 100 % D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPKDU[U-98% 13C; U-98% 15N]1
10 mMsodium phosphate1
200 mMpotassium chloride1
50 uMEDTA1
95 %H2O1
5 %D2O1
1 mMPKDU[U-98% 13C; U-98% 15N]2
10 mMsodium phosphate2
200 mMpotassium chloride2
50 uMEDTA2
100 %D2O2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.3 ambient 283 K
26.3 ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE8003

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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
MOLMOL2k.2Koradi, Billeter and Wuthrichdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: PDB entry 2k96 is a better refined structure of entry 1ymo with additional RDCs
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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