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- PDB-1jfw: HOMONUCLEAR AND HETERONUCLEAR 1H-13C NUCLEAR MAGNETIC RESONANCE A... -

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Basic information

Entry
Database: PDB / ID: 1jfw
TitleHOMONUCLEAR AND HETERONUCLEAR 1H-13C NUCLEAR MAGNETIC RESONANCE ASSIGNMENT AND STRUCTURAL CHARACTERIZATION OF A HIV-1 TAT PROTEIN
ComponentsTAT PROTEIN
KeywordsVIRAL PROTEIN / TAT / HIV-1 / HETERONUCLEAR / DRUG DESIGN
Function / homology
Function and homology information


modulation of transcription in other organism involved in symbiotic interaction / trans-activation response element binding / modulation by virus of host PP1 activity / RNA-binding transcription regulator activity / negative regulation of cellular respiration / modulation by virus of host chromatin organization / host cell nucleolus / membrane hyperpolarization / actinin binding / positive regulation of viral transcription ...modulation of transcription in other organism involved in symbiotic interaction / trans-activation response element binding / modulation by virus of host PP1 activity / RNA-binding transcription regulator activity / negative regulation of cellular respiration / modulation by virus of host chromatin organization / host cell nucleolus / membrane hyperpolarization / actinin binding / positive regulation of viral transcription / negative regulation of peptidyl-threonine phosphorylation / cyclin binding / positive regulation of transcription elongation from RNA polymerase II promoter / positive regulation of protein localization to nucleus / positive regulation of NF-kappaB transcription factor activity / suppression by virus of host type I interferon-mediated signaling pathway / transcription, DNA-templated / host cell cytoplasm / protein domain specific binding / extracellular region / metal ion binding
Similarity search - Function
HIV-1 Transactivator Protein / Tat domain / Tat domain superfamily / Transactivating regulatory protein (Tat) / Immunodeficiency virus transactivating regulatory protein (Tat) / Few Secondary Structures / Irregular
Similarity search - Domain/homology
MethodSOLUTION NMR / SIMULATED ANNEALING, RANDOM LOOP RESEARCH VALIDATED WITH NOE BACK-CALCULATION ENERGY MINIMIZATION, MOLECULAR DYNAMIC
AuthorsPeloponese, J.M. / Gregoire, C. / Opi, S. / Esquieu, D.
CitationJournal: C.R.Acad.Sci.III / Year: 2000
Title: 1H-13C nuclear magnetic resonance assignment and structural characterization of HIV-1 Tat protein.
Authors: Peloponese Jr., J.M. / Gregoire, C. / Opi, S. / Esquieu, D. / Sturgis, J. / Lebrun, E. / Meurs, E. / Collette, Y. / Olive, D. / Aubertin, A.M. / Witvrow, M. / Pannecouque, C. / De Clercq, E. ...Authors: Peloponese Jr., J.M. / Gregoire, C. / Opi, S. / Esquieu, D. / Sturgis, J. / Lebrun, E. / Meurs, E. / Collette, Y. / Olive, D. / Aubertin, A.M. / Witvrow, M. / Pannecouque, C. / De Clercq, E. / Bailly, C. / Lebreton, J. / Loret, E.P.
History
DepositionJun 22, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionAug 15, 2001ID: 1FKU
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)9,7891
Polymers9,7891
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100BACK CALCULATED DATA AGREE WITH EXPERIMEN TAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY, TARGET FUNCTION
Representative

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Components

#1: Protein TAT PROTEIN / TRANSACTIVATING REGULATORY PROTEIN


Mass: 9789.319 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS SYNTHESIZED (SOLID PHASE SYNTHESIS). THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
References: UniProt: P04610

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1313D 13C-SEPARATED NOESY

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Sample preparation

DetailsContents: SPECIFIC 13C LABELLING OF GLYCINE 15,44,48,61,79,83
Sample conditionspH: 4.50 / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DISCOVER 95, 97MSIrefinement
FELIX95structure solution
97 AND98structure solution
NMR_REFINE97structure solution
HOMOLOGY95structure solution
97structure solution
98structure solution
RefinementMethod: SIMULATED ANNEALING, RANDOM LOOP RESEARCH VALIDATED WITH NOE BACK-CALCULATION ENERGY MINIMIZATION, MOLECULAR DYNAMIC
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 915 RESTRAINTS AND 272 ARE LONG-RANGE NOES.
NMR ensembleConformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMEN TAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE ...Conformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMEN TAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY, TARGET FUNCTION
Conformers calculated total number: 100 / Conformers submitted total number: 11

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