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- PDB-2a9x: TAR RNA recognition by a cyclic peptidomimetic of Tat protein -

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Basic information

Entry
Database: PDB / ID: 2a9x
TitleTAR RNA recognition by a cyclic peptidomimetic of Tat protein
Components
  • BIV TAR RNA
  • BIV-2 cyclic peptide
KeywordsRNA binding protein/RNA / NMR / peptidomimetics / peptide structure / RNA recognition / immunodeficiency virus / TAR RNA / RNA binding protein-RNA COMPLEX
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Torsion Angle Molecular Dynamics
AuthorsLeeper, T.C. / Athanassiou, Z. / Dias, R.L. / Robinson, J.A. / Varani, G.
CitationJournal: Biochemistry / Year: 2005
Title: TAR RNA recognition by a cyclic peptidomimetic of Tat protein.
Authors: Leeper, T.C. / Athanassiou, Z. / Dias, R.L. / Robinson, J.A. / Varani, G.
History
DepositionJul 12, 2005Deposition site: RCSB / Processing site: RCSB
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: BIV TAR RNA
1: BIV-2 cyclic peptide


Theoretical massNumber of molelcules
Total (without water)10,6772
Polymers10,6772
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: RNA chain BIV TAR RNA


Mass: 8923.310 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was transcribed in vitro from DNA oligonucleotide templates with T7 RNA polymerase purified in house with unlabeled or 13C/15N enriched NTPs (Silantes) and purified by denaturing PAGE.
#2: Protein/peptide BIV-2 cyclic peptide


Mass: 1754.162 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The BIV-2 peptide was synthesized by solid phase synthesis and purified by reverse phase HPLC
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
132(H)CCH-COSY
142(H)CCH-TOCSY
252HNN-COSY
162F1fF2f-type 2D TOCSY
172F1fF2f-type 2D NOESY
282F1fF2f-type 2D NOESY
1923D 31P HETCOR etc
1102IPAP-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM BIV-2 peptide plus unlabeled 0.8 mM BIV TAR RNA, 20 mM Sodium Acetate, D3, pH 5.0, 100% D2O20 mM Sodium Acetate, D3, pH 5.0, 100% D2O
20.8 mM BIV-2 peptide plus unlabeled 0.8 mM BIV TAR RNA, 20 mM Sodium Acetate, D3, pH 5.0, 90% H2O, 10% D2O20 mM Sodium Acetate, D3, pH 5.0, 90% H2O, 10% D2O
30.6 mM BIV-2 peptide plus 13C/15N labeled 0.6 mM BIV TAR RNA, 20 mM Sodium Acetate, D3, pH 5.0, 100% D2O20 mM Sodium Acetate, D3, pH 5.0, 100% D2O
40.6 mM BIV-2 peptide plus 13C/15N labeled 0.6 mM BIV TAR RNA, 20 mM Sodium Acetate, D3, pH 5.0, 90% H2O, 10% D2O20 mM Sodium Acetate, D3, pH 5.0, 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM Na+ 51 atm298 K
220 mM Na+ 51 atm275 K

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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 DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
NMRPipe2.3Delaglio et alprocessing
X-PLOR2.9Schwieters et alstructure solution
Sparky3.11Goddard and Knellerdata analysis
X-PLOR2.9Schwieters et alrefinement
RefinementMethod: Torsion Angle Molecular Dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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