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- PDB-2pn9: NMR structure of a kissing complex formed between the TAR RNA ele... -

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Basic information

Entry
Database: PDB / ID: 2pn9
TitleNMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer
Components
  • 5'-R(*GP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*C)-3'
  • RNA 16-mer with locked residues 9-10
KeywordsRNA / LNA / Locked Nucleic Acid / NMR / Aptamer / TAR / HIV-1 / kissing
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsLebars, I. / Richard, T. / Di Primo, C. / Toulme, J.-J.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer
Authors: Lebars, I. / Richard, T. / Di Primo, C. / Toulme, J.-J.
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*C)-3'
B: RNA 16-mer with locked residues 9-10


Theoretical massNumber of molelcules
Total (without water)10,3042
Polymers10,3042
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)10 / 100The submitted structure are the 10 structures with zero violation on NOE distance, dihedral and with the lowest energy.
RepresentativeModel #1closest to the average

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Components

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


Mass: 5168.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
#2: RNA chain RNA 16-mer with locked residues 9-10


Mass: 5136.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Aptamer was purchased from Eurogentec

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
115HSQC
1263D (H)CCH-TOCSY
1332D NOESY
1442D NOESY
1542D TOCSY
1643D NOESY-NOESY
NMR detailsText: The structure was determined using standard homonulear and heteronuclear methods.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM unlabeled TAR10 mM phosphate buffer pH 6.4; 90% H2O, 10% D2O
21 mM unlabeled aptamer10 mM phosphate buffer pH 6.4; 90% H2O, 10% D2O
31 mM unlabeled TAR/aptamer complex10 mM phosphate buffer pH 6.4; 90% H2O, 10% D2O
41 mM unlabeled TAR/aptamer complex10 mM phosphate buffer pH 6.4; 100% D2O
51 mM 15N/13C labeled TAR/unlabeled aptamer complex10 mM phosphate buffer pH 6.4; 90% H2O, 10% D2O
61 mM 15N/13C labeled TAR/unlabeled aptamer complex10 mM phosphate buffer pH 6.4; 100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.4ambient 288 K
26.4ambient 277 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger A. T. etallstructure solution
CNS1.1Brunger A. T. etallrefinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted structure are the 10 structures with zero violation on NOE distance, dihedral and with the lowest energy.
Conformers calculated total number: 100 / Conformers submitted total number: 10

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