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- PDB-2n28: Solid-state NMR structure of Vpu -

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Basic information

Entry
Database: PDB / ID: 2n28
TitleSolid-state NMR structure of Vpu
ComponentsProtein Vpu
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
Protein Vpu / Protein Vpu
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLID-STATE NMR / simulated annealing
Model detailslowest energy, model1
AuthorsZhang, H. / Lin, E.C. / Tian, Y. / Das, B.B. / Opella, S.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Structural determination of virus protein U from HIV-1 by NMR in membrane environments.
Authors: Zhang, H. / Lin, E.C. / Das, B.B. / Tian, Y. / Opella, S.J.
History
DepositionMay 1, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Vpu


Theoretical massNumber of molelcules
Total (without water)9,1481
Polymers9,1481
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 Protein Vpu / U ORF protein / Viral protein U


Mass: 9147.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: vpu / Plasmid: pET31b+ / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P69700, UniProt: P69699*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 13C/13C PDSD
1212D 13C/15N HETCOR
1312D 13C/13C TOBSY
1412D 13C-1H DC/13C SLF
1512D 15N-1H DC/13C SLF
1613D 15N/13CA/13C
1713D 15N/13C'/13C
1813D 1H-15N DC/15N/13CA SLF
1913D 1H-13C DC/15N/13CA SLF

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Sample preparation

DetailsContents: 8.5 mM [U-100% 13C; U-100% 15N] HIV-1 Virus protein U, 100% H2O
Solvent system: 100%H2O
SampleConc.: 8.5 mM / Component: HIV-1 Virus protein U-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 20 / pH: 7.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger, A.T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE ANI COORDINATES HAVE BEEN INCLUDED IN THE RESTRAINT FILE. THE ANI Z AXIS SPECIFIES THE DIRECTION OF THE NORMAL TO THE PLANE OF THE LIPID BILAYER MEMBRANE.
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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