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- PDB-1nz1: Solution structure of the S. cerevisiae U6 Intramolecular stem-lo... -

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Basic information

Entry
Database: PDB / ID: 1nz1
TitleSolution structure of the S. cerevisiae U6 Intramolecular stem-loop containing an SP phosphorothioate at nucleotide U80
ComponentsSP U6 Intramolecular Stem-Loop RNA
KeywordsRNA / U6 RNA / stem-loop / phosphorothioate / Sp phosphorothioate / residual dipolar coupling / RDC
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Torsion angle, molecular dynamics, simulated annealing, residual dipolar coupling
AuthorsReiter, N.J. / Nikstad, L.J. / Allman, A.M. / Johnson, R.J. / Butcher, S.E.
CitationJournal: RNA / Year: 2003
Title: Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.
Authors: Reiter, N.J. / Nikstad, L.J. / Allman, A.M. / Johnson, R.J. / Butcher, S.E.
History
DepositionFeb 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 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: SP U6 Intramolecular Stem-Loop RNA


Theoretical massNumber of molelcules
Total (without water)7,6851
Polymers7,6851
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)17 / 100structures with the lowest energy
RepresentativeModel #15lowest energy

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Components

#1: RNA chain SP U6 Intramolecular Stem-Loop RNA / SP ISL RNA


Mass: 7684.681 Da / Num. of mol.: 1 / Mutation: A62G / Source method: obtained synthetically
Details: Synthetic RNA (Dharmacon, Inc.) was prepared containing an SP phosphorothioate modification at nucleotide U80. The Sp RNA was separated from the Rp RNA diastereomer using reverse-phase high ...Details: Synthetic RNA (Dharmacon, Inc.) was prepared containing an SP phosphorothioate modification at nucleotide U80. The Sp RNA was separated from the Rp RNA diastereomer using reverse-phase high pressure liquid chromatography.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
222HSQC
333HSQC
3432D NOESY
3532D TOCSY
NMR detailsText: Solution structure based on 322 NOE derived distance restraints, 144 dihedral angle restraints, 25 hydrogen bond restraints, and 40 residual dipolar copupling restraints.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.2 mM RNA, 50 mM NaCL, pH 7.0H2O
20.8-1.2 mM RNA, 50 mM NaCL, pH 7.0, 17 mg/mL PF1 PhageH2O
30.8-1.2 mM RNA, 50 mM NaCL, pH 7.0D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 7.0 ambient 283 K
250 mM NaCl 7.2 ambient 303 K
350 mM NaCl 7.0 ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DMXBrukerDMX7501
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX5003
Bruker DMXBrukerDMX4004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Felix98Accelrysprocessing
Sparky3Goddard, T.D. and D.G. Knellerdata analysis
CNS1.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: Torsion angle, molecular dynamics, simulated annealing, residual dipolar coupling
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 17

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