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- PDB-2rp1: Refined solution structure of the PEMV-1 mRNA pseudoknot, regular... -

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Basic information

Entry
Database: PDB / ID: 2rp1
TitleRefined solution structure of the PEMV-1 mRNA pseudoknot, regularized average structure
ComponentsPEMV-1 mRNA pseudoknot
KeywordsRNA / RNA pseudoknot / frameshifting
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsCornish, P.V. / Hennig, M. / Giedroc, D.P.
CitationJournal: Virus Res. / Year: 2009
Title: Frameshifting RNA pseudoknots: Structure and mechanism.
Authors: Giedroc, D.P. / Cornish, P.V.
History
DepositionApr 25, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: 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 / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
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: PEMV-1 mRNA pseudoknot


Theoretical massNumber of molelcules
Total (without water)8,6721
Polymers8,6721
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)1 / 28structures with the lowest energy
Representativeminimized average structure

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Components

#1: RNA chain PEMV-1 mRNA pseudoknot


Mass: 8672.255 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was produced by in vitro transcription using SP6 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY
1212D 1H-1H NOESY
133J-MODULATED CT-HSQC
143CT-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM RNA, 10 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM DSS, 5 mM magnesium chloride, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-100% 13C; U-100% 15N] RNA, 10 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM DSS, 5 mM magnesium chloride, 100% D2O100% D2O
32 mM [U-100% 13C; U-100% 15N] RNA, 10 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM DSS, 20 mg/ml Pf1 phage, 5 mM magnesium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMRNA (27-MER)1
10 mMpotassium phosphate1
100 mMpotassium chloride1
.1 mMDSS1
5 mMmagnesium chloride1
2 mMRNA (27-MER)[U-100% 13C; U-100% 15N]2
10 mMpotassium phosphate2
100 mMpotassium chloride2
.1 mMDSS2
5 mMmagnesium chloride2
2 mMRNA (27-MER)[U-100% 13C; U-100% 15N]3
10 mMpotassium phosphate3
100 mMpotassium chloride3
.1 mMDSS3
20 %Pf1 phage3
5 mMmagnesium chloride3
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Varian INOVAVarianINOVA5003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorerefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
FelixAccelrys Software Inc.peak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 28 / Conformers submitted total number: 1 / Representative conformer: 1

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