+Open data
-Basic information
Entry | Database: PDB / ID: 1tac | ||||||
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Title | HIV-1 TAT CYS-, NMR, 10 STRUCTURES | ||||||
Components | TAT PROTEIN | ||||||
Keywords | TRANSCRIPTION REGULATION / HIV-1 / TRANSACTIVATION / RNA BINDING | ||||||
Function / homology | Function and homology information viral gene expression / trans-activation response element binding / protein serine/threonine phosphatase inhibitor activity / regulatory region RNA binding / positive regulation of viral transcription / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / actinin binding / negative regulation of peptidyl-threonine phosphorylation ...viral gene expression / trans-activation response element binding / protein serine/threonine phosphatase inhibitor activity / regulatory region RNA binding / positive regulation of viral transcription / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / actinin binding / negative regulation of peptidyl-threonine phosphorylation / 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 / virus-mediated perturbation of host defense response / DNA-templated transcription / apoptotic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS | ||||||
Authors | Roesch, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tac.cif.gz | 270.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tac.ent.gz | 223.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/1tac ftp://data.pdbj.org/pub/pdb/validation_reports/ta/1tac | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: H2O/D2O (9:1) |
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Sample conditions | Ionic strength: 0.85 M / pH: 5 / Pressure: 10E+5 PA atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz |
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-Processing
Software |
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NMR software |
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Refinement | Method: 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 ensemble | Conformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA Conformers calculated total number: 240 / Conformers submitted total number: 10 |