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

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Basic information

Entry
Database: PDB / ID: 2oom
TitleNMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA/RNA aptamer
Components
  • RNA 16-mer
  • TAR RNA element of HIV-1
KeywordsRNA / LNA / Locked Nucleic Acid / NMR / Aptamer / TAR / HIV-1
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
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq
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 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3Dec 27, 2023Group: 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: RNA 16-mer
B: TAR RNA element of HIV-1


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)12 / 100The submitted structures are the 12 structures with zero violation on NOE distance, dihedral and with the lowest energy.
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA 16-mer


Mass: 5168.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: prepared by in vitro transcription with T7 RNA polymerase
#2: RNA chain TAR RNA element of HIV-1


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1142D NOESY
1242D TOCSY
134DQF-COSY
146HMQC
1563D HMQC-NOESY
1663D (H)CCH-TOCSY
1743D NOESY-NOESY
183NOESY
195HSQC
21032D NOESY
NMR detailsText: The structure was determined using standard homonuclear and heteronuclear methods

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM unlabeled TAR; 10mM phosphate buffer pH 6.490% H2O/10% D2O
21 mM unlabeled aptamer; 10mM phosphate buffer pH 6.490% H2O/10% D2O
31 mM unlabeled TAR/aptamer complex; 10mM phosphate buffer pH 6.490% H2O/10% D2O
41 mM unlabeled TAR/aptamer complex; 10mM phosphate buffer pH 6.4100% D2O
51 mM 15N,13C TAR/unlabeled,aptamer complex; 10mM phosphate buffer pH 6.490% H2O/10% D2O
61 mM 15N,13C TAR/unlabeled,aptamer complex; 10mM phosphate100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.4 ambient 288 K
26.4 ambient 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 softwareName: CNS / Version: 1.1 / Developer: Brunger A. T. etall / Classification: refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted structures are the 12 structures with zero violation on NOE distance, dihedral and with the lowest energy.
Conformers calculated total number: 100 / Conformers submitted total number: 12

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