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- PDB-1pjy: Solution structure of the HIV-1 frameshift inducing stem-loop RNA -

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Entry
Database: PDB / ID: 1pjy
TitleSolution structure of the HIV-1 frameshift inducing stem-loop RNA
ComponentsHIV-1 frameshift inducing stem-loop
KeywordsRNA / frameshift / HIV / tetraloop / RNA structure
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle molecular dynamics, Cartesian space simulated annealing, molecular dynamics, residual dipolar coupling
AuthorsStaple, D.W. / Butcher, S.E.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: Solution structure of the HIV-1 frameshift inducing stem-loop RNA.
Authors: Staple, D.W. / Butcher, S.E.
History
DepositionJun 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: HIV-1 frameshift inducing stem-loop


Theoretical massNumber of molelcules
Total (without water)7,0711
Polymers7,0711
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)20 / 100Submitted confermers represent the 20 lowest energy structures with no NOE violations greater than 0.2 Angstroms and no dihedral violations greater than 5 degrees
RepresentativeModel #1lowest energy

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Components

#1: RNA chain HIV-1 frameshift inducing stem-loop


Mass: 7071.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 RNA transcript from synthetic DNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3112D NOESY
3212D TOCSY
3313D 13C-separated NOESY
2412D HNN-COSY
1512D NOESY
3612D 1H-13C HSQC
NMR detailsText: The incorporation of residual dipolar couplings and the direct detection of hydrogen bonds with HNN-COSY were used in solving this structure

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Sample preparation

DetailsContents: 1 mM HIV-1 frameshift inducing stem-loop RNA / Solvent system: 90% H2O/10% D2O, or 99.99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM 6.8 ambient 283 K
250 mM 6.8 ambient 298 K
350 mM 6.8 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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6collection
CNS1.1Brungerrefinement
Felix98processing
Sparky3.72data analysis
RefinementMethod: torsion angle molecular dynamics, Cartesian space simulated annealing, molecular dynamics, residual dipolar coupling
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Submitted confermers represent the 20 lowest energy structures with no NOE violations greater than 0.2 Angstroms and no dihedral violations greater than 5 degrees
Conformers calculated total number: 100 / Conformers submitted total number: 20

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