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- PDB-2jtp: Solution Structure of the Frameshift-Inducing RNA Stem-Loop in SIV -

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Basic information

Entry
Database: PDB / ID: 2jtp
TitleSolution Structure of the Frameshift-Inducing RNA Stem-Loop in SIV
ComponentsSIV17-50 RNA (34-MER)
KeywordsRNA / SIV / RNA Stem-Loop / Triloop / Frameshifting / HIV-2
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics, residual dipolar couplings
AuthorsMarcheschi, R.J. / Staple, D.W. / Butcher, S.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Programmed Ribosomal Frameshifting in SIV Is Induced by a Highly Structured RNA Stem-Loop
Authors: Marcheschi, R.J. / Staple, D.W. / Butcher, S.E.
History
DepositionAug 4, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: SIV17-50 RNA (34-MER)


Theoretical massNumber of molelcules
Total (without water)10,9131
Polymers10,9131
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain SIV17-50 RNA (34-MER)


Mass: 10912.575 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcription 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
1122D 1H-1H TOCSY
1222D 1H-1H NOESY
1312D 1H-1H COSY
1442D 1H-15N HSQC
1542D 1H-13C HSQC
1643D 1H-13C-1H (H)CCH-TOCSY
1743D NOESY-HMQC
183J-MODULATED 1H-13C CT-HSQC
193J-MODULATED 1H-13C CT-HSQC
11012D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM SIV17-50 RNA (34-MER), 90% H2O/10% D2O90% H2O/10% D2O
21 mM SIV17-50 RNA (34-MER), 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER), 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] SIV17-50 RNA (34-MER), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSIV17-50 RNA (34-MER)1
1 mMSIV17-50 RNA (34-MER)2
1 mMSIV17-50 RNA (34-MER)[U-100% 13C; U-100% 15N]3
1 mMSIV17-50 RNA (34-MER)[U-100% 13C; U-100% 15N]4
Sample conditionspH: 7 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX6002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004
Bruker DMXBrukerDMX5005
Varian INOVAVarianINOVA9006

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
Sparky3.111Goddardpeak picking
Sparky3.111Goddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
VNMRVariancollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics, residual dipolar couplings
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: 20

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