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- PDB-1zbn: Solution structure of BIV TAR hairpin complexed to JDV Tat argini... -

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Basic information

Entry
Database: PDB / ID: 1zbn
TitleSolution structure of BIV TAR hairpin complexed to JDV Tat arginine-rich motif
Components
  • BIV mRNA
  • JDV tat protein
KeywordsRNA binding protein/RNA / RNA-peptide complex / RNA binding protein-RNA COMPLEX
Function / homology
Function and homology information


positive regulation of viral transcription / host cell nucleolus / RNA-binding transcription regulator activity / viral process / 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
MethodSOLUTION NMR / distance geometry, restrained molecular dynamics
AuthorsCalabro, V. / Daugherty, M.D. / Frankel, A.D.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: A single intermolecular contact mediates intramolecular stabilization of both RNA and protein.
Authors: Calabro, V. / Daugherty, M.D. / Frankel, A.D.
#1: Journal: Mol.Cell / Year: 2000
Title: An RNA-binding chameleon
Authors: Smith, C.A. / Calabro, V. / Frankel, A.D.
#2: Journal: Science / Year: 1995
Title: Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex
Authors: Puglisi, J.D. / Chen, L. / Blanchard, S. / Frankel, A.D.
History
DepositionApr 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: BIV mRNA
B: JDV tat protein


Theoretical massNumber of molelcules
Total (without water)10,9882
Polymers10,9882
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 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain BIV mRNA


Mass: 8923.310 Da / Num. of mol.: 1 / Mutation: A4G, U31C / Source method: obtained synthetically
Details: This sequence occurs naturally in Bovine immunodeficiency virus (BIV).
#2: Protein/peptide JDV tat protein


Mass: 2064.493 Da / Num. of mol.: 1 / Fragment: Arginine-rich domain / Source method: obtained synthetically
Details: This sequence occurs naturally in Jembrana disease virus (JDV).
References: UniProt: Q82854*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112DQF-COSY
1222D TOCSY
1322D NOESY
3422D NOESY
2512D NOESY
1612D TOCSY
171DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM RNA, 1.5mM peptide, 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM RNA, 1.5mM peptide, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl, 10mM sodium phosphate 6.5 ambient 290 K
250mM NaCl, 10mM sodium phosphate 6.5 ambient 285 K
350mM NaCl, 10mM sodium phosphate 6.5 ambient 300 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.xGuentertstructure solution
CNS1.1Brungerrefinement
NMRPipeNADelaglioprocessing
Sparky3Goddarddata analysis
RefinementMethod: distance geometry, restrained molecular dynamics / Software ordinal: 1
Details: Structures were calculated beginning with 1,000 random structures and incrementally adding distance constraints in four iterations. The final 30 structures with the lowest number of ...Details: Structures were calculated beginning with 1,000 random structures and incrementally adding distance constraints in four iterations. The final 30 structures with the lowest number of violations were subjected to RMD. The structures are based on a total of 700 distance constraints, 61 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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