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- PDB-2mtj: NMR structure of the III-IV-V three-way junction from the VS ribozyme -

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Basic information

Entry
Database: PDB / ID: 2mtj
TitleNMR structure of the III-IV-V three-way junction from the VS ribozyme
ComponentsRNA (47-MER)
KeywordsRNA / VS ribozyme / Three-way junction / Base triple / U-turn Ribose zipper / GAAA tetraloop / CUUG tetraloop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBonneau, E. / Legault, P.
CitationJournal: Biochemistry / Year: 2014
Title: Nuclear Magnetic Resonance Structure of the III-IV-V Three-Way Junction from the Varkud Satellite Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement.
Authors: Bonneau, E. / Legault, P.
History
DepositionAug 19, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Data collection / Derived calculations / Experimental preparation
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / struct_conn
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening ..._ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (47-MER)


Theoretical massNumber of molelcules
Total (without water)15,1181
Polymers15,1181
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)21 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (47-MER)


Mass: 15117.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Neurospora crassa (fungus)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D flip-back WATERGATE 1H
1212D 1H-15N HSQC
1312D 1H-15N HSQC NH2 only
1413D 1H-15N NOESY
2522D 1H-13C HSQC
2623D 13C-edited HMQC-NOESY
2723D CT-(H)CCH-COSY
2823D (H)CCH-TOCSY
2933D 15N-edited NOESY-HSQC
21032D H(NC)-TOCSY-(C)H for guanosine residues
21122D 1H-13C HMQC
21222D 1H-15N MQ-(HC)N(C)H
11312D 1H-15N CPMG-NOESY
11412D HNN-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5-2.0 mM [U-100% 15N] J345-1-1, 5mM MgCl2, 90% H2O/10% D2O90% H2O/10% D2O
22.0 mM [U-100% 13C; U-100% 15N] J345-2-2, 5mM MgCl2, 100% D2O100% D2O
32.0 mM [U-100% 13C; U-100% 15N] J345-3-3, 5mM MgCl2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingConc. range (mg/ml)Solution-ID
2 mMJ345-1-1[U-100% 15N]1.5-2.01
2.0 mMJ345-2-2[U-100% 13C; U-100% 15N]2
2.0 mMJ345-3-3[U-100% 13C; U-100% 15N]3
5 mMMgCl2-14
5 mMMgCl2-25
5 mMMgCl2-36
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
155 6.5 288 K
255 6.5 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPNMR_suiteCCPNchemical shift assignment
CCPNMR_suiteCCPNdata analysis
CCPNMR_suiteCCPNpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
PyMOLSchrodingerstructure analysis
PyMOLSchrodingerstructure display
RefinementMethod: simulated annealing / 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: 21

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