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- PDB-1xhp: Solution Structure of the Extended U6 ISL as Observed in the U2/U... -

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Basic information

Entry
Database: PDB / ID: 1xhp
TitleSolution Structure of the Extended U6 ISL as Observed in the U2/U6 complex from Saccharomyces cerevisiae
ComponentsU6 snRNA
KeywordsRNA / U6 RNA / RNA stem-loop / penta-loop / internal bulge / metal binding site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics, residual dipolar couplings, conformational database potentials
AuthorsSashital, D.G. / Cornilescu, G. / Butcher, S.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction
Authors: Sashital, D.G. / Cornilescu, G. / McManus, C.J. / Brow, D.A. / Butcher, S.E.
History
DepositionSep 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 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: U6 snRNA


Theoretical massNumber of molelcules
Total (without water)10,2401
Polymers10,2401
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain U6 snRNA


Mass: 10240.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcription of U6 nucleotides 59-88 using purified T7 RNA polymerase and synthetic DNA oligonucleotides.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2322D TOCSY
2443D 13C-separated NOESY
2543D [1H-13C-1H] (H)CCH-TOCSY
4643D [1H-13C-1H] (H)CCH -COSY
3732D [15N-1H] HNN-COSY
285J-MODULATED [13C-1H] CT-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM extended U6 ISL RNA; 90% H2O; 10% D2O90% H2O/10% D2O
21mM extended U6 ISL RNA; 99.99% D2O99.99% D2O
31mM 13C,15N labeled extended U6 ISL RNA; 90% H2O; 10% D2O90% H2O/10% D2O
41mM 13C,15N labeled extended U6 ISL RNA; 99.99% D2O99.99% D2O
51mM 13C,15N labeled extended U6 ISL RNA; 17 mg/ml pf1 bacteriophage; 90% H2O; 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHTemperature (K)
16.9283 K
27.5303 K
36.9298 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 DMXBrukerDMX6001
Bruker DMXBrukerDMX7502
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukerprocessing
VNMR1.1Varianprocessing
NMRPipe97.027.12.56Baxprocessing
Sparky3.105Goddard and Knellerdata analysis
CNS1.1Brungerstructure solution
XPLOR-NIH2.9.7Clore, Kuszewski, Schwieters, Tjandrastructure solution
XPLOR-NIH2.9.7refinement
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics, residual dipolar couplings, conformational database potentials
Software ordinal: 1
Details: 435 NOE distance constraints, 244 dihedral angle restraints, 66 hydrogen bond restraints, 77 residual dipolar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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