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- PDB-1osw: The Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein ... -

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Entry
Database: PDB / ID: 1osw
TitleThe Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop
Components5'-R(*GP*GP*AP*GP*GP*CP*GP*CP*UP*AP*CP*GP*GP*CP*GP*AP*GP*GP*CP*UP*CP*CP*A)-3'
KeywordsRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DYANA, molecular dynamics using AMBER
AuthorsYuan, Y. / Kerwood, D.J. / Paoletti, A.C. / Shubsda, M.F. / Borer, P.N.
CitationJournal: Biochemistry / Year: 2003
Title: Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop
Authors: Yuan, Y. / Kerwood, D.J. / Paoletti, A.C. / Shubsda, M.F. / Borer, P.N.
History
DepositionMar 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,4731
Polymers7,4731
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)23 / 50structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #17closest to the average

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Components

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


Mass: 7472.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA sequence obtained from Dharmacon

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131HP-COSY
2412D NOESY
151H-C HSQC
NMR detailsText: Structures were determined using 2D NOESY at different temperatures and mixing times. The last residue, A23, was eliminated from the pdb file due to ambiguity in orientation.

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Sample preparation

DetailsContents: 1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3
Solvent system: 99.996% D2O or 90% D2O, 10% H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125 mM NaCl 6.3ambient 300 K
225 mM NaCl 5.5ambient 278 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
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRZ/TRIAD6.1Triposprocessing
MARDIGRAS3.2University of California, San Franciscoiterative matrix relaxation
DYANA1.5Guntert, P., Mumenthaler, C. and Wuthrich, K.structure solution
Amber5University of California, San Franciscorefinement
RefinementMethod: DYANA, molecular dynamics using AMBER / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 50 / Conformers submitted total number: 23

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