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- PDB-2k95: Solution structure of the wild-type P2B-P3 pseudoknot of human te... -

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Entry
Database: PDB / ID: 2k95
TitleSolution structure of the wild-type P2B-P3 pseudoknot of human telomerase RNA
ComponentsTelomerase RNA P2b-P3 pseudoknot
KeywordsRNA / telomerase / pseudoknot / triple helix / bulge / 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 (mature hTR RNA ...A unimolecular pseudoknot construct composed of nucleotides 95-116 and 166-183 (mature hTR RNA numbering system)
AuthorsKim, N.-K. / Zhang, Q. / Zhou, J. / Theimer, C.A. / Peterson, R.D. / Feigon, J.
CitationJournal: 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.
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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase RNA P2b-P3 pseudoknot


Theoretical massNumber of molelcules
Total (without water)15,2891
Polymers15,2891
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: 15289.085 Da / Num. of mol.: 1 / Fragment: Wild-type P2b-P3 pseudoknot / 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 (mature hTR RNA numbering system)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 11ECHO NOESY
1212D WATERGATE NOESY
2342D 1H-13C S3CT HSQC
2462D 1H-13C HSQC
2582D 1H-13C HSQC
1632D 15N CPMG NOESY
2722D TOCSY
1832D 15N HMQC
2962D NOESY
21082D NOESY
11132D JNN-HNN COSY
21242D (H)CCH COSY
21343D (H)CCH-TOCSY
21442D 13C filtered/edited NOESYs
21543D 13C HSQC NOESY
11632D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM PKWT, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O95% H2O/5% D2O
21 mM PKWT, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 100 % D2O100% D2O
31 mM [U-98% 13C; U-98% 15N] PKWT, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O95% H2O/5% D2O
41 mM [U-98% 13C; U-98% 15N] PKWT, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 100 % D2O100% D2O
51 mM [U-13C; U-15N]-Ade, [U-13C; U-15N]-Ura PKWT, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O, 0.2 % sodium azide95% H2O/5% D2O
61 mM [U-13C; U-15N]-Ade, [U-13C; U-15N]-Ura PKWT, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 100 % D2O, 0.2 % sodium azide100% D2O
71 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Cyt PKWT, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O, 0.2 % sodium azide95% H2O/5% D2O
81 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Cyt PKWT, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 100 % D2O, 0.2 % sodium azide100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPKWT1
10 mMsodium phosphate1
200 mMpotassium chloride1
50 uMEDTA1
95 %H2O1
5 %D2O1
1 mMPKWT2
10 mMsodium phosphate2
200 mMpotassium chloride2
50 uMEDTA2
100 %D2O2
1 mMPKWT[U-98% 13C; U-98% 15N]3
10 mMsodium phosphate3
200 mMpotassium chloride3
50 uMEDTA3
95 %H2O3
5 %D2O3
1 mMPKWT[U-98% 13C; U-98% 15N]4
10 mMsodium phosphate4
200 mMpotassium chloride4
50 uMEDTA4
100 %D2O4
1 mMPKWT[U-13C; U-15N]-Ade, [U-13C; U-15N]-Ura5
10 mMsodium phosphate5
200 mMpotassium chloride5
50 uMEDTA5
95 %H2O5
5 %D2O5
0.2 %sodium azide5
1 mMPKWT[U-13C; U-15N]-Ade, [U-13C; U-15N]-Ura6
10 mMsodium phosphate6
200 mMpotassium chloride6
50 uMEDTA6
100 %D2O6
0.2 %sodium azide6
1 mMPKWT[U-13C; U-15N]-Gua, [U-13C; U-15N]-Cyt7
10 mMsodium phosphate7
200 mMpotassium chloride7
50 uMEDTA7
95 %H2O7
5 %D2O7
0.2 %sodium azide7
1 mMPKWT[U-13C; U-15N]-Gua, [U-13C; U-15N]-Cyt8
10 mMsodium phosphate8
200 mMpotassium chloride8
50 uMEDTA8
100 %D2O8
0.2 %sodium azide8
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
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
XwinNMR3.5Bruker Biospinchemical shift assignment
XwinNMR3.5Bruker Biospinprocessing
XwinNMR3.5Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
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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