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- PDB-2qh4: Solution structure of the U85 C/D-H/ACA scaRNA 5' terminal hairpi... -

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Basic information

Entry
Database: PDB / ID: 2qh4
TitleSolution structure of the U85 C/D-H/ACA scaRNA 5' terminal hairpin loop
ComponentsHuman U85 C/D-H/ACA scaRNA
KeywordsRNA / loop / sheared GA pair
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsFeigon, J. / Theimer, C.A. / Chim, N. / Breece, K.E.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural and functional characterization of human telomerase RNA processing and cajal body localization signals.
Authors: Theimer, C.A. / Jady, B.E. / Chim, N. / Richard, P. / Breece, K.E. / Kiss, T. / Feigon, J.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: 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: Human U85 C/D-H/ACA scaRNA


Theoretical massNumber of molelcules
Total (without water)5,7881
Polymers5,7881
Non-polymers00
Water0
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 violation, consistent with residual dipolar couplings
RepresentativeModel #1lowest energy

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Components

#1: RNA chain Human U85 C/D-H/ACA scaRNA


Mass: 5788.491 Da / Num. of mol.: 1 / Fragment: U85 5' terminal hairpin loop / Source method: obtained synthetically
Details: RNA is synthesized using in vitro transcription with T7 RNA polymerase and a partially double-stranded DNA template

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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, Natural abundance 2D 13C HSQC
1322D 15N-HMQC, 2D 15N-CPMG-NOESY, 2D JNN-HNN-COSY
2422D 13C-HSQC, 2D (H)CCH-COCSY, 3D (H)CCH-TOCSY, 3D NOESY-HMQC, 2D 31P spin echo difference (H)CCH/HSQC/HMQC, 2D CT-CE-HSQC
1532D 15N-HMQC
2632D 13C-HSQC, 2D filtered-edited NOESYs

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM unlabeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 100 mM KCl, 50 uM EDTA, 0.2% sodium azide; 95% H2O, 5% D2O or 100% D2O95% H2O, 5% D2O or 100% D2O
21 mM 13C, 15N labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 100 mM KCl, 50 uM EDTA, 0.2% sodium azide; 95% H2O, 5% D2O or 100% D2O95% H2O, 5% D2O or 100% D2O
31 mM 13C, 15N G-only labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 100 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)
1100 mM KCl 6.3 ambient 283 K
2100 mM KCl 6.3 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
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
AURELIA3.108Brungerdata analysis
X-PLOR3.851NIHstructure solution
X-PLOR3.851NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures are based on 404 NOE-derived distance contraints, 70 dihedral angle restraints, and 18 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, no restraint violation, consistent with residual dipolar couplings
Conformers calculated total number: 200 / Conformers submitted total number: 20

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