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- PDB-1pje: Structure of the channel-forming trans-membrane domain of Virus p... -

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Basic information

Entry
Database: PDB / ID: 1pje
TitleStructure of the channel-forming trans-membrane domain of Virus protein "u"(Vpu) from HIV-1
ComponentsVPU protein
KeywordsVIRAL PROTEIN / ALPHA-HELIX
Function / homology
Function and homology information


receptor catabolic process / CD4 receptor binding / viral release from host cell / host cell membrane / monoatomic cation channel activity / symbiont-mediated-mediated suppression of host tetherin activity / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane
Similarity search - Function
Vpu protein / Vpu protein cytoplasmic domain superfamily / Vpu protein
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodSOLID-STATE NMR / Direct structural fitting of 2D solid-state NMR data
AuthorsPark, S.H. / Mrse, A.A. / Nevzorov, A.A. / Mesleh, M.F. / Oblatt-Montal, M. / Montal, M. / Opella, S.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Three-dimensional structure of the channel-forming trans-membrane domain of Virus protein "u" (Vpu) from HIV-1
Authors: Park, S.H. / Mrse, A.A. / Nevzorov, A.A. / Mesleh, M.F. / Oblatt-Montal, M. / Montal, M. / Opella, S.J.
History
DepositionJun 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: VPU protein


Theoretical massNumber of molelcules
Total (without water)3,8741
Polymers3,8741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100minimized average structure
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide VPU protein / U ORF protein


Mass: 3873.885 Da / Num. of mol.: 1 / Fragment: Trans-membrane domain / Mutation: Y29G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: VPU / Plasmid: pET-31b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS / References: UniProt: Q70625

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experimentType: PISEMA
NMR detailsText: PISEMA: Polarization Inversion Spin Exchange at the Magic Angle

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Sample preparation

DetailsContents: Completely aligned sample in glass plates: 3.5 mg Vpu2-30+ U-15N, 75 mg lipid mixture (DOPC:DOPG, 9:1)
Sample conditionspH: 7 / Pressure: ambient / Temperature: 293 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: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
Structural Fitting1Nevzorov, Opellastructure solution
Structural Fitting1Nevzorov, Opellarefinement
RefinementMethod: Direct structural fitting of 2D solid-state NMR data
Software ordinal: 1
Details: This structure was calculated by using a structural fitting algorithm that finds torsion angles between consecutive residues based on their NMR frequencies
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: minimized average structure / Conformers calculated total number: 100 / Conformers submitted total number: 1

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