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- PDB-1kzv: Structure of Human Immunodeficiency Virus Type 1 Vpr(34-51) Pepti... -

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Basic information

Entry
Database: PDB / ID: 1kzv
TitleStructure of Human Immunodeficiency Virus Type 1 Vpr(34-51) Peptide in Chloroform Methanol
ComponentsVpr PROTEIN
KeywordsVIRAL PROTEIN / HIV-1 / Vpr / solution structure / chloroform / methanol
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / virion component / symbiont-mediated activation of host apoptosis / protein homooligomerization / 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 / virion component / symbiont-mediated activation of host apoptosis / protein homooligomerization / 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 / apoptotic process
Similarity search - Function
Retroviral VpR/VpX protein / VPR/VPX protein
Similarity search - Domain/homology
MethodSOLUTION NMR / simulated annealing
AuthorsEngler, A. / Stangler, T. / Willbold, D.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Structure of human immunodeficiency virus type 1 Vpr(34-51) peptide in micelle containing aqueous solution.
Authors: Engler, A. / Stangler, T. / Willbold, D.
History
DepositionFeb 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)2,2721
Polymers2,2721
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)20 / 60structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Vpr PROTEIN


Mass: 2271.578 Da / Num. of mol.: 1 / Fragment: RESIDUES 34-51 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS Chemically synthesized. IT IS NATURALLY FOUND IN human immunodeficiency virus type 1 (New York-5 isolate) (HIV-1).
References: UniProt: P12520

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2 mM Vpr(34-51); 50 % Methanol d3, 50 % Chloroform d1
Solvent system: 50 % Methanol d3, 50 % Chloroform d1
Sample conditionsIonic strength: 0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
VNMR5.3Variancollection
NDEESpinUp Inc.data analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: structures were calculated using floating chirality.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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