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- PDB-1lvj: STRUCTURE OF TAR RNA COMPLEXED WITH A TAT-TAR INTERACTION NANOMOL... -

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Basic information

Entry
Database: PDB / ID: 1lvj
TitleSTRUCTURE OF TAR RNA COMPLEXED WITH A TAT-TAR INTERACTION NANOMOLAR INHIBITOR THAT WAS IDENTIFIED BY COMPUTATIONAL SCREENING
ComponentsHIV-1 Trans Activating Region RNA
KeywordsRNA / Transcriptional Activation / Complex (RNA-drug)
Function / homologyChem-PMZ / RNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing starting from random coordinates
AuthorsDu, Z. / Lind, K.E. / James, T.L.
CitationJournal: CHEM.BIOL. / Year: 2002
Title: Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening
Authors: Du, Z. / Lind, K.E. / James, T.L.
History
DepositionMay 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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: HIV-1 Trans Activating Region RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2842
Polymers9,9581
Non-polymers3261
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 / 12least violations and lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain HIV-1 Trans Activating Region RNA


Mass: 9957.942 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: IN Vitro Transcription
#2: Chemical ChemComp-PMZ / 1-[10-(3-DIMETHYLAMINO-PROPYL)-10H-PHENOTHIAZIN-2-YL]-ETHANONE / ACETYLPROMAZINE


Mass: 326.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2OS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY, 3D 13C-seperated NOESY, 3D 15N-seperated NOESY

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Sample preparation

DetailsContents: 10 mM sodium phosphate (pH 6.5), 20mM sodium Chloride
Solvent system: 90% H2O, 10% D2O or 100% H2O
Sample conditionsIonic strength: 30 mM / pH: 6.5 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.6Guntertstructure solution
Amber6Pearlman et al.refinement
Sparky3Goddarddata analysis
RefinementMethod: simulated annealing starting from random coordinates
Software ordinal: 1
Details: The structure was determined by multidimentional heteronuclear NMR spectroscopy on a unlabeled, a 15N,13C-labeled sample and three type-specific (A,G or C) labeled samples.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: least violations and lowest energy
Conformers calculated total number: 12 / Conformers submitted total number: 12

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