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- PDB-1m8l: NMR structure of the HIV-1 Regulatory Protein Vpr -

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Basic information

Entry
Database: PDB / ID: 1m8l
TitleNMR structure of the HIV-1 Regulatory Protein Vpr
ComponentsVPR Protein
KeywordsVIRAL PROTEIN / Vpr / CD3CN / HIV-1
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 / apoptotic process
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
AuthorsMorellet, N. / Bouaziz, S. / Lenoir, C. / Roques, B.P.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: NMR Structure of the HIV-1 Regulatory Protein Vpr
Authors: Morellet, N. / Bouaziz, S. / Lenoir, C. / Roques, B.P.
History
DepositionJul 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: 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_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model
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)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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein VPR Protein


Mass: 11411.905 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence 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
1212D TOCSY
131HSQC-NOESY
141HSQC-TOCSY
1513D HSQC-NOESY
1613D HSQC-TOCSY
NMR detailsText: This structure was determined using standard 2D and 3D homonuclear and heteronuclear techniques

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Sample preparation

DetailsContents: 1 mM Vpr 70% H2O, 30% CD3CN pH 2.6 / Solvent system: 70% H2O, 30% CD3CN
Sample conditionspH: 2.6 / Pressure: ambient / Temperature: 303 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR3Brukercollection
UXNMR3Brukerdata analysis
Discover98msirefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total 1115 restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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