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- PDB-5kqe: Solution structure of P2a-J2a/b-P2b of medaka telomerase RNA -

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Basic information

Entry
Database: PDB / ID: 5kqe
TitleSolution structure of P2a-J2a/b-P2b of medaka telomerase RNA
ComponentsTelomerase RNA P2ab
KeywordsRNA / Telomerase RNA TR Medaka P2ab
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesOryzias latipes (Japanese medaka)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Y. / Feigon, J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM48123 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112503 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112294 United States
National Science Foundation (NSF, United States)MCB1517625 United States
Department of Energy (DOE, United States)DE-FC03-02ER63421 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human.
Authors: Wang, Y. / Yesselman, J.D. / Zhang, Q. / Kang, M. / Feigon, J.
History
DepositionJul 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase RNA P2ab


Theoretical massNumber of molelcules
Total (without water)11,4651
Polymers11,4651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 P2ab


Mass: 11464.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oryzias latipes (Japanese medaka)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-1H NOESY
123isotropic12D 1H-1H TOCSY
234isotropic12D 1H-1H NOESY
244isotropic12D 1H-1H TOCSY
155isotropic22D 1H-15N HSQC
265isotropic22D 1H-13C HSQC
172isotropic23D (H)CCH-TOCSY
282isotropic22D filtered/edited NOESY
193isotropic32D DQF-COSY
1103isotropic2JNN-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution510 mM sodium phosphate, 100 mM potassium chloride, 1.0 mM [U-13C; U-15N] Telomerase RNA P2ab, 90% H2O/10% D2Olabelled sample13C_15N_H2O90% H2O/10% D2O
solution210 mM sodium phosphate, 100 mM potassium chloride, 1.0 mM [U-13C; U-15N] Telomerase RNA P2ab, 100% D2Olabelled sample13C_15N_D2O100% D2O
solution310 mM sodium phosphate, 100 mM potassium chloride, 1.0 mM Telomerase RNA P2ab, 90% H2O/10% D2Ounlabelled sampleH2O90% H2O/10% D2O
solution410 mM sodium phosphate, 100 mM potassium chloride, 1.0 mM Telomerase RNA P2ab, 100% D2Ounlabelled sampleD2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance5
100 mMpotassium chloridenatural abundance5
1.0 mMTelomerase RNA P2ab[U-13C; U-15N]5
10 mMsodium phosphatenatural abundance2
100 mMpotassium chloridenatural abundance2
1.0 mMTelomerase RNA P2ab[U-13C; U-15N]2
10 mMsodium phosphatenatural abundance3
100 mMpotassium chloridenatural abundance3
1.0 mMTelomerase RNA P2abnatural abundance3
10 mMsodium phosphatenatural abundance4
100 mMpotassium chloridenatural abundance4
1.0 mMTelomerase RNA P2abnatural abundance4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mMconditions_2836.4 1 atm283 K
2100 mMconditions_2986.4 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIH2.42Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 6
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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