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- PDB-1tac: HIV-1 TAT CYS-, NMR, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1tac
TitleHIV-1 TAT CYS-, NMR, 10 STRUCTURES
ComponentsTAT PROTEIN
KeywordsTRANSCRIPTION REGULATION / HIV-1 / TRANSACTIVATION / RNA BINDING
Function / homology
Function and homology information


viral gene expression / trans-activation response element binding / regulatory region RNA binding / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / symbiont-mediated perturbation of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / actinin binding / RNA-binding transcription regulator activity ...viral gene expression / trans-activation response element binding / regulatory region RNA binding / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / symbiont-mediated perturbation of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / actinin binding / RNA-binding transcription regulator activity / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein domain specific binding / DNA-templated transcription / extracellular region / metal ion binding
Similarity search - Function
HIV-1 Transactivator Protein / Tat domain / Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsRoesch, P. / Boehm, M. / Sticht, H.
Citation
Journal: To be Published
Title: Solution Structure of HIV-1 Tat Protein
Authors: Boehm, M. / Sticht, H. / Seidel, G. / Roesch, P.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Structural Studies of HIV-1 Tat Protein
Authors: Bayer, P. / Kraft, M. / Ejchart, A. / Westendorp, M. / Frank, R. / Rosch, P.
History
DepositionMar 13, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
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: TAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,5631
Polymers9,5631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 240ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
RepresentativeModel #1

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Components

#1: Protein TAT PROTEIN / TRANSACTIVATING REGULATORY PROTEIN


Mass: 9562.662 Da / Num. of mol.: 1 / Mutation: M1L, C22S, C25A, C27A, C30S, C31A, C34S, C37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Gene: TATCYS- / Variant: ZAIRE 2 / Plasmid: BL21 / Species (production host): Escherichia coli / Gene (production host): TATCYS- / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12506

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
1411H-15N-HSQC
1511H
1611H
17115N-NOESY-HMQC
1811H
1911H
110115N-TOCSY-HMQC

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Sample preparation

DetailsContents: H2O/D2O (9:1)
Sample conditionsIonic strength: 0.85 M / pH: 5 / Pressure: 10E+5 PA atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
NDEEstructure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: DESCRIPTION OF THE STRATEGY USED FOR NMR STRUCTURE CALCULATION AND REFINEMENT: NOE CROSS-PEAKS WERE DIVIDED INTO THREE CATEGORIES AND ASSIGNED DISTANCE RANGES ACCORDING TO THEIR INTENSITY: STRONG (<0.29 NM); MEDIUM (<0.42 NM); WEAK (<0.57 NM). PEAK INTENSITIES WERE ESTIMATED FROM THE NUMBER OF CONTOURS IN NOESY SPECTRUM. 23 3JHNA COUPLING CONSTANTS WERE EXTRACTED FROM DQF-COSY SPECTRUM, AND CONVERTED TO PHI-ANGLES ACCORDING THE KARPLUS EQUATION. THE STRUCTURE CALCULATIONS USED MODIFIED AB INITIO SIMULATED ANNEALING (SA. INP) AND REFINEMENT (REFINE. INP) PROTOCOLS FROM THE X-PLOR PROGRAM PACKAGE WHICH INCLUDED FLOATING ASSIGNMENT OF PROCHIRAL GROUPS, REDUCED PRESENTATION FOR NON-BOND INTERACTIONS FOR PART OF THE CALCULATION, REFINEMENT AGAINST CONFORMATIONAL DATABASE AND DIRECT REFINEMENT AGAINST 3JHNA COUPLING CONSTANTS. IN EACH ROUND OF STRUCTURE CALCULATION, 100 STRUCTURES WERE CALCULATED FROM TEMPLATES WITH RANDOM BACKBONE TORSION ANGLES. IN THE CONFORMATIONAL SEARCH PHASE 60 PS OF MOLECULAR DYNAMICS WERE SIMULATED AT 2000 K. THE REFINEMENT COMPRISED A TWO-PHASE COOLING PROCEDURE TREATING THE NON-BONDED INTERACTIONS BETWEEN ALL ATOMS BY A REPULSIVE ('REPEL') POTENTIAL. IN THE FIRST REFINEMENT STAGE, THE SYSTEM WAS COOLED FROM 2000 K TO 1000 K WITHIN 135 PS, CONCOMITANTLY INCREASING THE FORCE CONSTANTS TO THEIR FINAL VALUES. IN THE NEXT STAGE OF THE CALCULATION THE SYSTEM WAS COOLED FROM 1000 K TO 100 K WITHIN 90 PS, APPLYING THE HIGH FORCE CONSTANTS OBTAINED AT THE END OF THE PREVIOUS COOLING STAGE. DURING ALL STAGES OF THE CALCULATION A TIMESTEP OF 3 FS WAS USED. THEN, 500 STEPS OF POWELL ENERGY MINIMIZATION WERE PERFORMED, USING AN ATTRACTIVE LENARD-JONES POTENTIAL, BUT NO EXPLICIT ELECTROSTATICS AND RAMACHANDRAN DATABASIS POTENTIAL. OF THE 240 RESULTING STRUCTURES, THOSE 10 STRUCTURES THAT SHOWED THE LOWEST ENERGY AND THE LEAST VIOLATION OF THE EXPERIMENTAL DATA WERE SELECTED FOR FURTHER CHARACTERIZATION. GEOMETRY OF THE STRUCTURES AND ELEMENTS OF SECONDARY STRUCTURE WERE ANALYZED USING PROCHECK AND DSSP.
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 240 / Conformers submitted total number: 10

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