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- PDB-1ju1: Dimer Initiation Sequence of HIV-1Lai Genomic RNA: NMR Solution S... -

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Basic information

Entry
Database: PDB / ID: 1ju1
TitleDimer Initiation Sequence of HIV-1Lai Genomic RNA: NMR Solution Structure of the Extended Duplex
ComponentsHIV-1Lai SL1
KeywordsRNA / HIV / dimer initiation sequence / SL1 / extended duplex / stable dimer
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, matrix relaxation
AuthorsGirard, F. / Barbault, F. / Lancelot, G.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1999
Title: Dimer initiation sequence of HIV-1Lai genomic RNA: NMR solution structure of the extended duplex.
Authors: Girard, F. / Barbault, F. / Gouyette, C. / Huynh-Dinh, T. / Paoletti, J. / Lancelot, G.
History
DepositionAug 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 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: HIV-1Lai SL1
B: HIV-1Lai SL1


Theoretical massNumber of molelcules
Total (without water)14,8352
Polymers14,8352
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)15 / 15back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #11lowest energy

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Components

#1: RNA chain HIV-1Lai SL1


Mass: 7417.488 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM oligonucleotide, 10mM phosphate buffer 100 mM NaCl90% H2O/10% D2O
22mM oligonucleotide, 10mM phosphate buffer, 100 mM NaCl100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NaCl 5.8ambient 278 K
2100mM NaCl 5.8ambient 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMRcollection
UXNMRprocessing
X-PLOR3.851Brungerstructure solution
Curves5Laverydata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing, matrix relaxation / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 15 / Conformers submitted total number: 15

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