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- PDB-2m21: Solution structure of the Tetrahymena telomerase RNA stem IV term... -

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Basic information

Entry
Database: PDB / ID: 2m21
TitleSolution structure of the Tetrahymena telomerase RNA stem IV terminal loop
Components5'-R(*GP*GP*CP*GP*AP*UP*AP*CP*AP*CP*UP*AP*UP*UP*UP*AP*UP*CP*GP*CP*C)-3'
KeywordsRNA / holoenzyme / protozoan proteins / ciliate / template / genetic / reverse transcriptase
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsCash, D.D. / Richards, R.J. / Wu, H. / Trantirek, L. / O'Connor, C.M. / Feigon, J. / Collins, K.
CitationJournal: Rna / Year: 2006
Title: Structural study of elements of Tetrahymena telomerase RNA stem-loop IV domain important for function.
Authors: Richards, R.J. / Wu, H. / Trantirek, L. / O'Connor, C.M. / Collins, K. / Feigon, J.
History
DepositionDec 11, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
SupersessionMay 1, 2013ID: 2H2X
Revision 1.1May 1, 2013Group: Advisory
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*CP*GP*AP*UP*AP*CP*AP*CP*UP*AP*UP*UP*UP*AP*UP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,6501
Polymers6,6501
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)14 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(*GP*GP*CP*GP*AP*UP*AP*CP*AP*CP*UP*AP*UP*UP*UP*AP*UP*CP*GP*CP*C)-3'


Mass: 6649.980 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11111echo and WATERGATE
2212D TOCSY
2312D NOESY
1422D 15N-HMQC, 2D 15N-CPMG-NOESY, 2D JNN-HNN-COSY
2522D 13C-HSQCs
2622D (H)CCH COSY, 3D (H)CCH-TOCSY
2723D 1H,13C HMQCs

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-1.0 mM unlabeled RNA (5'-R(*GP*GP*CP*GP*AP*UP*AP*CP*AP*CP*UP*AP*UP*UP*UP*AP*UP*CP*GP*CP*C)-3'), 20 mM potassium chloride, 0.2 % sodium azide, 50 uM EDTA, 10 mM sodium phosphate, 90% H2O/10% D2O or 100% D2O90% H2O/10% D2O or 100% D2O
20.6-1.0 mM 13C,15N uniformly labelled RNA (5'-R(*GP*GP*CP*GP*AP*UP*AP*CP*AP*CP*UP*AP*UP*UP*UP*AP*UP*CP*GP*CP*C)-3'), 10 mM sodium phosphate, 20 mM potassium chloride, 0.2 % sodium azide, 50 uM EDTA, 90% H2O/10% D2O or 100% D2O90% H2O/10% D2O or 100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (5'-R(*GP*GP*CP*GP*AP*UP*AP*CP*AP*CP*UP*AP*UP*UP*UP*AP*UP*CP*GP*CP*C)-3')-1unlabeled0.6-1.01
20 mMpotassium chloride-21
0.2 %sodium azide-31
50 uMEDTA-41
10 mMsodium phosphate-51
mMRNA (5'-R(*GP*GP*CP*GP*AP*UP*AP*CP*AP*CP*UP*AP*UP*UP*UP*AP*UP*CP*GP*CP*C)-3')-613C,15N uniformly labelled0.6-1.02
10 mMsodium phosphate-72
20 mMpotassium chloride-82
0.2 %sodium azide-92
50 uMEDTA-102
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1206.3ambient 298 K
2206.3ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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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
SparkyGoddarddata analysis
SparkyGoddardpeak picking
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: residual polar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 14

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