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- PDB-1ow9: NMR Structure of the Active Conformation of the VS Ribozyme Cleav... -

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Basic information

Entry
Database: PDB / ID: 1ow9
TitleNMR Structure of the Active Conformation of the VS Ribozyme Cleavage Site
ComponentsA mimic of the VS Ribozyme Hairpin Substrate
KeywordsRNA / VS ribozyme / substrate hairpin / cleavage site / sheared G-A base pairs / shared sheared G-A base pairs / magnesium ion binding / GNRA tetraloop / riboze zipper
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics; simulated annealing
Model type detailsminimized average
AuthorsHoffmann, B. / Mitchell, G.T. / Gendron, P. / Major, F. / Andersen, A.A. / Collins, R.A. / Legault, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: NMR Structure of the Active Conformation of the Varkud satellite Ribozyme Cleavage Site
Authors: Hoffmann, B. / Mitchell, G.T. / Gendron, P. / Major, F. / Andersen, A.A. / Collins, R.A. / Legault, P.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: A mimic of the VS Ribozyme Hairpin Substrate


Theoretical massNumber of molelcules
Total (without water)7,4891
Polymers7,4891
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)11 / 50structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain A mimic of the VS Ribozyme Hairpin Substrate / SL1


Mass: 7488.577 Da / Num. of mol.: 1 / Fragment: VS RNA substrate hairpin / Source method: obtained synthetically
Details: This sequence is derived from the Neurospora VS ribozyme substrate

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C/15N-edited HSQC-NOESY
1223D 13C-edited HMQC-NOESY
1332D 1H/15N CPMG-NOESY
1432D HNN-COSY
1542D H(CN)N(H)
1652D DQF-COSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM RNA U-13C,15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN390% H2O/10% D2O
21.1 mM RNA U-13C,15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN3100% D2O
31.7 mM RNA U-15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN390% H2O/10% D2O
45.3 mM RNA U-15N; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05mM NaN390% H2O/10% D2O
51.7 mM RNA; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN3100% D2O
61.7 mM RNA; 10 mM d11-Tris pH 7.0; 50 mM NaCl; 0.2 mM EDTA; 0.05 mM NaN390% H2O/10% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglioprocessing
NMRView5.03Johnsondata analysis
X-PLOR3.84Brungerstructure solution
MOLMOL2K.1Koradidata analysis
X-PLOR3.84Brungerrefinement
RefinementMethod: restrained molecular dynamics; simulated annealing / Software ordinal: 1
Details: the first model is the minimized average structure, the last 10 represent the ensemble of structures
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 11

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