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- PDB-1esy: NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIG... -

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Entry
Database: PDB / ID: 1esy
TitleNMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM
ComponentsRNA (5'-R(P*GP*GP*CP*GP*AP*CP*UP*GP*GP*UP*GP*AP*GP*UP*AP*CP*GP*CP*C)-3')
KeywordsRNA / HIV-1 / Splice-donor site / platform motif
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Distance Geometry, Simulated annealing, Energy mimimization
AuthorsAmarasinghe, G.K. / De Guzman, R.N. / Turner, R.B. / Summers, M.F.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform.
Authors: Amarasinghe, G.K. / De Guzman, R.N. / Turner, R.B. / Summers, M.F.
History
DepositionApr 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(P*GP*GP*CP*GP*AP*CP*UP*GP*GP*UP*GP*AP*GP*UP*AP*CP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,1491
Polymers6,1491
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: RNA chain RNA (5'-R(P*GP*GP*CP*GP*AP*CP*UP*GP*GP*UP*GP*AP*GP*UP*AP*CP*GP*CP*C)-3')


Mass: 6148.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 Transcript

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
2322D NOESY
3413D 13C-separated NOESY
3513D 13C-separated ROESY
NMR detailsText: experimental temperature set to either 298 or 278

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-1.2 mM SL2 RNA, Natural abundance, 25 mM Na-d3-acetate buffer100% D2O
20.6-1.2 mM SL2 RNA, Natural abundance, 25 mM Na-d3-acetate buffer90% H2O/10% D2O
30.6-1.2 mM SL2 RNA, U-15N,13C; 25 mM Na-d3-acetate buffer100% D2O
Sample conditionsIonic strength: 25 mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruckercollection
NMRPipe1Delaglio, Gresiek, Vuister, Zhu, and Baxprocessing
NMRView3Johnson, and Blevinsdata analysis
DYANA1.5Guntert and Mumenthalerstructure solution
CNS1Brunger et al.refinement
RefinementMethod: Distance Geometry, Simulated annealing, Energy mimimization
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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