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- PDB-2ke6: Solution Structure of K10 TLS RNA -

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Basic information

Entry
Database: PDB / ID: 2ke6
TitleSolution Structure of K10 TLS RNA
ComponentsK10 TLS RNA
KeywordsRNA / RNA transport / RNA hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing, restrained molecular dynamics with RDCs
Model detailslowest energy, model 1
AuthorsBullock, S.L. / Ringel, I. / Ish-Horowicz, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: A'-form RNA helices are required for cytoplasmic mRNA transport in Drosophila
Authors: Bullock, S.L. / Ringel, I. / Ish-Horowicz, D. / Lukavsky, P.J.
History
DepositionJan 23, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: 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 29, 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: K10 TLS RNA


Theoretical massNumber of molelcules
Total (without water)15,2551
Polymers15,2551
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)12 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain K10 TLS RNA


Mass: 15255.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PREPARED BY IN VITRO TRANSCRIPTION USING T7 / Source: (synth.) Drosophila melanogaster (fruit fly)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1322D 1H-1H TOCSY
1422D DQF-COSY
1522D HP COSY
1632D 1H-1H NOESY
1742D 1H-1H NOESY
1852D HNN COSY
1963D (H)CCH-TOCSY
11063D (H)CCH-COSY
11163D 13C NOESY-HSQC
11263D HCP
11363D 13C HMQC TOCSY
11462D 13C CT-TROSY
NMR detailsText: STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE, MULTIDIMENSIONAL NMR SPECTROSCOPY AND TROSY-TYPE EXPERIMENTS TO MEASURE RESIDUAL DIPOLAR COUPLINGS

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM K10 RNA; 95% H2O/5% D2O95% H2O/5% D2O
21.0mM K10 RNA; 100% D2O100% D2O
31.0mM K10 RNA; 95% H2O/5% D2O95% H2O/5% D2O
41.0mM K10 RNA; 100% D2O100% D2O
50.8mM [U-99% 13C; U-99% 15N] K10 RNA; 5% D2O95% H2O/5% D2O
60.8mM [U-99% 13C; U-99% 15N] K10 RNA; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMK10 RNA-1natural abundance1
1.0 mMK10 RNA-2pyrimidine H5-deuterated2
0.8 mMK10 RNA-3[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 0.01 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, restrained molecular dynamics with RDCs
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: 12 / Representative conformer: 1

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