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- PDB-1esx: 1H, 15N AND 13C STRUCTURE OF THE HIV-1 REGULATORY PROTEIN VPR : C... -

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Basic information

Entry
Database: PDB / ID: 1esx
Title1H, 15N AND 13C STRUCTURE OF THE HIV-1 REGULATORY PROTEIN VPR : COMPARISON WITH THE N-AND C-TERMINAL DOMAIN STRUCTURE, (1-51)VPR AND (52-96)VPR
ComponentsVPR PROTEIN
KeywordsVIRAL PROTEIN / helix / amphipatic / turn
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated activation of host apoptosis / protein homooligomerization / virion component / viral penetration into host nucleus / host cell / monoatomic ion transmembrane transport / host extracellular space / symbiont entry into host cell / DNA-templated transcription ...symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated activation of host apoptosis / protein homooligomerization / virion component / viral penetration into host nucleus / host cell / monoatomic ion transmembrane transport / host extracellular space / symbiont entry into host cell / DNA-templated transcription / regulation of DNA-templated transcription / host cell nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4730 / 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
MethodSOLUTION NMR / simulated annealing, molecular dynamics, minimisations
AuthorsWecker, K. / Morellet, N. / Bouaziz, S. / Roques, B.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: NMR structure of the HIV-1 regulatory protein Vpr in H2O/trifluoroethanol. Comparison with the Vpr N-terminal (1-51) and C-terminal (52-96) domains.
Authors: Wecker, K. / Morellet, N. / Bouaziz, S. / Roques, B.P.
History
DepositionApr 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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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)11,4121
Polymers11,4121
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 / 20structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #20fewest violations,lowest energy

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Components

#1: Protein VPR PROTEIN / VIRAL PROTEIN OF REGULATION


Mass: 11411.905 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence has been obtained by solid phase synthesis. The sequence of this protein is naturally found in Human immunodeficiency virus type 1 (HIV-1).
References: UniProt: Q73369

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131HSQC (15N, 13C)
141HSQC-NOESY (15N, 13C)
151HSQC-TOCSY(15N, 13C)
NMR detailsText: This structure was determined using standard 2D homonuclear techniques, 2D heteronuclear techniques and relaxation experiments

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Sample preparation

DetailsContents: 1 mM Vpr 15N, 13C ; 10 mM DTT ; HMDS ; 70 % H2O ; 30 % TFE
Solvent system: 70 % H20, 30 % TFE
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
103.4ambient 323 K
203.4ambient 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
Discover98msistructure solution
XwinNMR2.1brukercollection
Discover98msirefinement
XwinNMR2.1brukerprocessing
RefinementMethod: simulated annealing, molecular dynamics, minimisations
Software ordinal: 1
Details: The structure is based on a total of 1420 distance constraints
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 1

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