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- PDB-2goh: Three-dimensional Structure of the Trans-membrane Domain of Vpu f... -

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Basic information

Entry
Database: PDB / ID: 2goh
TitleThree-dimensional Structure of the Trans-membrane Domain of Vpu from HIV-1 in Aligned Phospholipid Bicelles
ComponentsVPU protein
KeywordsVIRAL PROTEIN / trans-membrane helix / 16C bicelles / magnetic alignment
Function / homology
Function and homology information


receptor catabolic process / CD4 receptor binding / viral release from host cell / host cell membrane / monoatomic cation channel activity / suppression by virus of host tetherin activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / apoptotic process / 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
Model type detailsminimized average
AuthorsPark, S.H. / De Angelis, A.A. / Nevzorov, A.A. / Wu, C.H. / Opella, S.J.
CitationJournal: Biophys.J. / Year: 2006
Title: Three-Dimensional Structure of the Transmembrane Domain of Vpu from HIV-1 in Aligned Phospholipid Bicelles.
Authors: Park, S.H. / De Angelis, A.A. / Nevzorov, A.A. / Wu, C.H. / Opella, S.J.
History
DepositionApr 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 4, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.temperature ..._pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 29, 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)3,7431
Polymers3,7431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100first 21 structures
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3742.689 Da / Num. of mol.: 1 / Fragment: Trans-membrane domain, residues 2-30 / Mutation: Y29G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: VPU / Plasmid: pET31-b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q70625, UniProt: Q2NN19*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: PISEMA

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Sample preparation

DetailsContents: 15N-uniformly or selectively peptide aligned in 16C bicelles (1,2-di-O-hexadecyl-sn-glycero-3-phosphocholine (16- O-PC) / 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (6-O-PC) = 3.0, 28% w/v, 100% H2O
Solvent system: 100% H2O
Sample conditionsPressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerManufacturer: Bruker / Field strength: 900 MHz

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Processing

NMR softwareName: Structural Fitting / Developer: Nevzorov, A.A. et al. / Classification: refinement
RefinementMethod: Structural fitting / Software ordinal: 1
Details: Orientational frequencies (15N chemical shift and 15N-1H dipolar coupling) for each amide site were used.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: first 21 structures / Conformers calculated total number: 100 / Conformers submitted total number: 21

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