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- PDB-2jpx: A18H Vpu TM structure in lipid bilayers -

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Basic information

Entry
Database: PDB / ID: 2jpx
TitleA18H Vpu TM structure in lipid bilayers
ComponentsVpu protein
KeywordsVIRAL PROTEIN / A18H Vpu / trans-membrane / ion-channel / helix tilt / lipid bilayers
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
Protein Vpu / Protein Vpu
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / structural fitting
AuthorsPark, S. / Opella, S.J.
CitationJournal: Protein Sci. / Year: 2007
Title: Conformational changes induced by a single amino acid substitution in the trans-membrane domain of Vpu: implications for HIV-1 susceptibility to channel blocking drugs
Authors: Park, S.H. / Opella, S.J.
History
DepositionMay 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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 / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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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)3,8101
Polymers3,8101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Vpu protein


Mass: 3809.758 Da / Num. of mol.: 1 / Mutation: A18H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH 10 isolate / Gene: vpu / Production host: Escherichia coli (E. coli) / References: UniProt: Q76PP7, UniProt: P69699*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 15N chemical shift/1H-15N dipolar coupling separated local field (SAMPI4)

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Sample preparation

DetailsContents: 2 mg/mL [U-99% 15N] A18H Vpu TM, 100% H2O / Solvent system: 100% H2O
SampleConc.: 2 mg/mL / Component: A18H Vpu TM / Isotopic labeling: [U-99% 15N]
Sample conditionsIonic strength: 0 / pH: 4 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
Structural FittingNevzorov and Opellastructure solution
Structural FittingNevzorov and Opellarefinement
RefinementMethod: structural fitting / Software ordinal: 1
Details: Nevzorov, A.A., and Opella, S.J. 2003. Structural fitting of PISEMA spectra of aligned proteins. J Magn Reson 160: 33-39.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 15

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