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- PDB-1vpc: C-TERMINAL DOMAIN (52-96) OF THE HIV-1 REGULATORY PROTEIN VPR, NM... -

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Basic information

Entry
Database: PDB / ID: 1vpc
TitleC-TERMINAL DOMAIN (52-96) OF THE HIV-1 REGULATORY PROTEIN VPR, NMR, 1 STRUCTURE
ComponentsVPR PROTEIN
KeywordsREGULATORY PROTEIN / HELICAL DOMAIN / LEUCINE-ZIPPER
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / monoatomic ion transmembrane transport / virion component / protein homooligomerization / viral penetration into host nucleus / host cell / host extracellular space / symbiont entry into host cell / cell cycle / DNA-templated transcription ...symbiont-mediated arrest of host cell cycle during G2/M transition / monoatomic ion transmembrane transport / virion component / protein homooligomerization / viral penetration into host nucleus / host cell / host extracellular space / symbiont entry into host cell / cell cycle / DNA-templated transcription / host cell nucleus / regulation of DNA-templated transcription
Similarity search - Function
VpR/VpX protein, C-terminal domain / Retroviral VpR/VpX protein / VPR/VPX protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING, MOLECULAR DYNAMICS, ENERGY MINIMIZATION
AuthorsSchueler, W. / De Rocquigny, H. / Baudat, Y. / Sire, J. / Roques, B.P.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: NMR structure of the (52-96) C-terminal domain of the HIV-1 regulatory protein Vpr: molecular insights into its biological functions.
Authors: Schuler, W. / Wecker, K. / de Rocquigny, H. / Baudat, Y. / Sire, J. / Roques, B.P.
History
DepositionFeb 20, 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 1.3Mar 2, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
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: VPR PROTEIN


Theoretical massNumber of molelcules
Total (without water)5,2571
Polymers5,2571
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)1 / 15LEAST RESTRAINT VIOLATIONS, LOWEST TOTAL ENERGY
Representative

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Components

#1: Protein/peptide VPR PROTEIN / VPR HIV-1 (LAI)


Mass: 5257.138 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 52-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: Q73369

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131E.COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H-NMR SPECTROSCOPY ON THE C-TERMINAL DOMAIN (52-96)VPR.

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Sample preparation

DetailsContents: 70% H2O 30% TFE
Sample conditionsIonic strength: LOW SALT CONDITIONS / pH: 3.4 / Pressure: 1 ATMOSPHERE / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
DiscoverBIOSYMrefinement
BRUKER UXNMRUXNMRstructure solution
BIOSYM/MSI FELIXFELIXstructure solution
RefinementMethod: DYNAMICAL SIMULATED ANNEALING, MOLECULAR DYNAMICS, ENERGY MINIMIZATION
Software ordinal: 1
Details: SEVENTY STRUCTURES WERE GENERATED BY SIMULATED ANNEALING AND FIFTEEN SELECTED STRUCTURES FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS (5PS 1000K, 10PS 600K, 55PS 300K) FOLLOWED BY ENERGY ...Details: SEVENTY STRUCTURES WERE GENERATED BY SIMULATED ANNEALING AND FIFTEEN SELECTED STRUCTURES FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS (5PS 1000K, 10PS 600K, 55PS 300K) FOLLOWED BY ENERGY MINIMIZATION. THE BEST STRUCTURE SELECTED WITH RESPECT TO RESTRAINT VIOLATIONS AND TOTAL ENERGY IS PRESENTED IN THIS ENTRY.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS, LOWEST TOTAL ENERGY
Conformers calculated total number: 15 / Conformers submitted total number: 1

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