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- PDB-1biv: BOVINE IMMUNODEFICIENCY VIRUS TAT-TAR COMPLEX, NMR, 5 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1biv
TitleBOVINE IMMUNODEFICIENCY VIRUS TAT-TAR COMPLEX, NMR, 5 STRUCTURES
Components
  • TAR RNA
  • TAT PEPTIDE
KeywordsViral protein/RNA / TAT-TAR / ARG-GUA INTERACTIONS / BUTTRESSING U(DOT)AU BASE TRIPLE / GLYCINE AND ISOLEUCINE PACKING / PEPTIDE RNA RECOGNITION / RNA BENDING / COMPLEX (RIBONUCLEIC ACID-PEPTIDE) / Viral protein-RNA COMPLEX
Function / homology
Function and homology information


positive regulation of viral transcription / host cell nucleolus / RNA-binding transcription regulator activity / RNA binding
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat)
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein Tat
Similarity search - Component
Biological speciessynthetic construct (others)
Bovine immunodeficiency virus
MethodSOLUTION NMR / molecular dynamics
AuthorsYe, X. / Kumar, R.A. / Patel, D.J.
CitationJournal: Chem.Biol. / Year: 1995
Title: Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex.
Authors: Ye, X. / Kumar, R.A. / Patel, D.J.
History
DepositionJun 12, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 25, 2016Group: Structure summary
Revision 1.4Aug 21, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_keywords
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity.src_method / _pdbx_database_status.process_site / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model / _struct_keywords.text
Revision 1.5Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAR RNA
B: TAT PEPTIDE


Theoretical massNumber of molelcules
Total (without water)10,8952
Polymers10,8952
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)5 / 5structures with acceptable covalent geometry and least restraint violations
Representative

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Components

#1: RNA chain TAR RNA


Mass: 8923.310 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE RNA WAS UNIFORMLY LABELLED WITH (13)C AND (15)N
Source: (synth.) synthetic construct (others)
#2: Protein/peptide TAT PEPTIDE


Mass: 1971.328 Da / Num. of mol.: 1 / Fragment: RESIDUES 65 - 81 / Source method: obtained synthetically / Source: (synth.) Bovine immunodeficiency virus / References: UniProt: P19564

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsLabel: sample conditions / pH: 6.8 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1FBRUNGERrefinement
CurvesLavery & Sklenardata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Restrained molecular dynamics calculations were performed on the Tat-TAR complex with a simulated annealing protocol in vacuum with a distance-dependent dielectric constant.
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry and least restraint violations
Conformers calculated total number: 5 / Conformers submitted total number: 5

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