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- PDB-1vpu: NMR SOLUTION STRUCTURE OF THE HIV-1 VPU CYTOPLASMIC DOMAIN, 9 STR... -

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Basic information

Entry
Database: PDB / ID: 1vpu
TitleNMR SOLUTION STRUCTURE OF THE HIV-1 VPU CYTOPLASMIC DOMAIN, 9 STRUCTURES
ComponentsVPU PROTEIN
KeywordsAIDS / HIV / VPU
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 / lipid binding / apoptotic process / 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 1
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsWillbold, D. / Hoffmann, S. / Rosch, P.
CitationJournal: Eur.J.Biochem. / Year: 1997
Title: Secondary structure and tertiary fold of the human immunodeficiency virus protein U (Vpu) cytoplasmic domain in solution.
Authors: Willbold, D. / Hoffmann, S. / Rosch, P.
History
DepositionJan 28, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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)5,1111
Polymers5,1111
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)9 / 25ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Representative

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Components

#1: Protein/peptide VPU PROTEIN / VPU(39-81)


Mass: 5111.440 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN RESIDUES 39 - 81 / Mutation: R37L, K38Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: SF162 ISOLATE / Cell line: BL21 / Gene: SYNTHETIC GENE / Plasmid: PET16B (NOVAGEN) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19554

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY (100
121150
131200 MS MIXING TIME)
NMR detailsText: REPRESENTATIVE MODEL NUMBER: 3

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Sample preparation

Sample conditionspH: 7 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameClassification
NDEEstructure solution
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 25 / Conformers submitted total number: 9

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