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- PDB-2d17: Solution RNA structure of stem-bulge-stem region of the HIV-1 dim... -

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Basic information

Entry
Database: PDB / ID: 2d17
TitleSolution RNA structure of stem-bulge-stem region of the HIV-1 dimerization initiation site
Components
  • 5'-R(*CP*GP*GP*CP*AP*AP*GP*AP*GP*GP*CP*GP*AP*CP*CP*C)-3'
  • 5'-R(*GP*GP*GP*UP*CP*GP*GP*CP*UP*UP*GP*CP*UP*G)-3'
KeywordsRNA / DIS / HIV-1
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsBaba, S. / Takahashi, K. / Noguchi, S. / Takaku, H. / Koyanagi, Y. / Yamamoto, N. / Kawai, G.
CitationJournal: J.Biochem.(Tokyo) / Year: 2005
Title: Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.
Authors: Baba, S. / Takahashi, K. / Noguchi, S. / Takaku, H. / Koyanagi, Y. / Yamamoto, N. / Kawai, G.
History
DepositionAug 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 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: 5'-R(*CP*GP*GP*CP*AP*AP*GP*AP*GP*GP*CP*GP*AP*CP*CP*C)-3'
B: 5'-R(*GP*GP*GP*UP*CP*GP*GP*CP*UP*UP*GP*CP*UP*G)-3'


Theoretical massNumber of molelcules
Total (without water)9,6862
Polymers9,6862
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)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 5174.190 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*GP*GP*GP*UP*CP*GP*GP*CP*UP*UP*GP*CP*UP*G)-3'


Mass: 4511.691 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
1241D-HSQC-selected spectrum
1341D-HSQC-filtered spectrum
1472D NOESY
2512D TOCSY
2612D NOESY
2732D-w2-filtered NOESY
2852D-w2-filtered NOESY
2962D TOCSY
21062D NOESY
NMR detailsText: Enzymatical synthesized 34-mer RNA corresponding to the stem-bulge-stem region of the HIV-1 dimerization initiation site. Enzymatical synthesized [G-13C/15N] labeled 39-mer RNA corresponding to ...Text: Enzymatical synthesized 34-mer RNA corresponding to the stem-bulge-stem region of the HIV-1 dimerization initiation site. Enzymatical synthesized [G-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized [A-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized 39-mer RNA corresponding to the HIV-1 dimerization initiation site.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM 34-mer RNA FRAGMENT; 10mM phosphate buffer, 50 mM NaCl; 100% D2O100% D2O
20.5mM 34-mer RNA FRAGMENT; 10mM phosphate buffer, 50 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
30.4mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50 mM NaCl; 100% D2O100% D2O
40.4mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
50.2mM [A-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50 mM NaCl; 100% D2O100% D2O
61.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50 mM NaCl; 100% D2O100% D2O
71.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl 7ambient 283 K
250mM NaCl 7ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERprocessing
Felix97Molecular Simulationsdata analysis
Discover97Accelrysstructure solution
Discover97Accelrysrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 529 restraints, 345 are NOE-derived distance constraints, 126 dihedral angle restraints, 58 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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