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- PDB-1ymo: Solution structure of the P2b-P3 pseudoknot from human telomerase RNA -

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Basic information

Entry
Database: PDB / ID: 1ymo
TitleSolution structure of the P2b-P3 pseudoknot from human telomerase RNA
ComponentsTelomerase RNA P2b-P3 pseudoknot
KeywordsRNA / pseudoknot / non-canonical / tertiary structure / Hoogsteen / triplex
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsTheimer, C.A. / Blois, C.A. / Feigon, J.
Citation
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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA
Authors: Theimer, C.A. / Finger, L.D. / Trantirek, L. / Feigon, J.
#2: Journal: RNA / Year: 2003
Title: YNMG tetraloop formation by a dyskeratosis congenita mutation in human telomerase RNA
Authors: Theimer, C.A. / Finger, L.D. / Feigon, J.
History
DepositionJan 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 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_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 1.4Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_database_related
Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
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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, no restraint violations, consistent with residual dipolar couplings
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
Details: RNA is synthesized using in vitro transcription with T7 RNA polymerase and a partially double-stranded DNA template. The sequence of this RNA can be found naturally in homo sapiens (human).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY (11echo and WATERGATE)
2212D NOESY, 2D TOCSY (presat)
1322D 15N-HMQC,2D 15N-CPMG-NOESY, 2D JNN-HNN-COSY
2422D 13C-HSQC
2532D 13C-HSQC, 2D (H)CCH COSY, 3D (H)CCH-TOCSY, 2D 13C filtered/edited NOESYs
2642D 13C-HSQC, 2D (H)CCH COSY, 3D (H)CCH-TOCSY, 2D 13C filtered/edited NOESYs
NMR detailsText: The same experiments were performed on all of the singly-labeled samples except for residual dipolar couplings which were only collected for the A- and G-only labeled samples.

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Sample preparation

Details
Solution-IDContentsSolvent system
1~0.8 mM unlabeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide, 95% H2O,5% D2O or 100% D2O95% H2O,5% D2O or 100% D2O
2~0.8 mM 13C,15N-fully labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide, 95% H2O,5% D2O or 100% D2O95% H2O,5% D2O or 100% D2O
3~0.8 mM 13C,15N-A labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide , 95% H2O,5% D2O or 100% D2O95% H2O,5% D2O or 100% D2O
4~0.8 mM 13C,15N-C labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide, 95% H2O,5% D2O or 100% D2O95% H2O,5% D2O or 100% D2O
5~0.8 mM 13C,15N-G labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide, 95% H2O,5% D2O or 100% D2O95% H2O,5% D2O or 100% D2O
6~0.8 mM 13C,15N-U labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide, 95% H2O,5% D2O or 100% D2O95% H2O,5% D2O or 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200 mM KCl 6.3 ambient 283 K
2200 mM KCl 6.3 ambient 293 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 DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
AURELIA3.108Brungerdata analysis
XPLOR-NIH1.0.6NIHstructure solution
XPLOR-NIH1.0.6NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures are based on 790 NOE-derived distance constraints, 210 dihedral angle restraints, 50 distance restraints from hydrogen bonds, and 20 H-C residual dipolar couplings. PDB entry PDB ...Details: Structures are based on 790 NOE-derived distance constraints, 210 dihedral angle restraints, 50 distance restraints from hydrogen bonds, and 20 H-C residual dipolar couplings. PDB entry PDB entry 2k96 is a better refined structure of entry 1ymo.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, no restraint violations, consistent with residual dipolar couplings
Conformers calculated total number: 200 / Conformers submitted total number: 20

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