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- PDB-2k7y: Solution fold of HIV-1 Virus protein U cytoplasmic domain in the ... -

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Basic information

Entry
Database: PDB / ID: 2k7y
TitleSolution fold of HIV-1 Virus protein U cytoplasmic domain in the presence of DPC micelles
ComponentsProtein Vpu
KeywordsVIRAL PROTEIN / PROTEIN / AIDS / Apoptosis / Host-virus interaction / Ion transport / Ionic channel / Membrane / Phosphoprotein / Transmembrane / Transport
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 / lipid binding / plasma membrane
Similarity search - Function
Cytoplasmic domain of VPU protein / HIV-1 VPU cytoplasmic domain / Vpu protein / Vpu protein cytoplasmic domain superfamily / Vpu protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWittlich, M. / Koenig, B.W. / Willbold, D.
CitationJournal: Febs J. / Year: 2009
Title: NMR structural characterization of HIV-1 virus protein U cytoplasmic domain in the presence of dodecylphosphatidylcholine micelles
Authors: Wittlich, M. / Koenig, B.W. / Stoldt, M. / Schmidt, H. / Willbold, D.
History
DepositionAug 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 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: Protein Vpu


Theoretical massNumber of molelcules
Total (without water)5,0141
Polymers5,0141
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Protein Vpu / Viral protein U / U ORF protein


Mass: 5014.283 Da / Num. of mol.: 1 / Fragment: VpU cytoplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HV1S1 / Gene: vpu / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P19554

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D C(CO)NH
1413D HN(CA)CB
1513D HN(CO)CA
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D HNHA
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] VpUcyt, 100 mM [U-100% 2H] DPC, 100 mM sodium chloride, 20 mM sodium phosphate, 0.02 w/v sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMVpUcyt[U-100% 13C; U-100% 15N]1
100 mMDPC[U-100% 2H]1
100 mMsodium chloride1
20 mMsodium phosphate1
0.02 w/vsodium azide1
Sample conditionsIonic strength: 100 / pH: 6.2 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4a.5Keller and Wuthrichdata analysis
CARA1.8.4a.5Keller and Wuthrichprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RADARHerrmann, Guntert, Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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