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- PDB-2d18: Solution RNA structure of loop region of the HIV-1 dimerization i... -

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Basic information

Entry
Database: PDB / ID: 2d18
TitleSolution RNA structure of loop region of the HIV-1 dimerization initiation site in the extended-duplex dimer
Components5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-3'
KeywordsRNA / DIS / HIV-1
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.
Validation Report
SummaryFull reportAbout validation report
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,9632
Polymers10,9632
Non-polymers00
Water0
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(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-3'


Mass: 5481.341 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
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: Chemical synthesized 25-mer RNA corresponding to 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
11.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O
21.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
30.4mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O
40.4mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
50.2mM [A-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O
61.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O
71.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions

Ionic strength: 50mM NaCl / pH: 7.0 / Pressure: ambient

Conditions-IDTemperature (K)
1283 K
2298 K

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NMR measurement

NMR spectrometer

Manufacturer: Bruker / Model: DRX / Type: Bruker DRX

Field strength (MHz)Spectrometer-ID
5001
6002

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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 598 restraints, 384 are NOE-derived distance constraints, 138 dihedral angle restraints, 76 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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