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- PDB-2n29: Solution-state NMR structure of Vpu cytoplasmic domain -

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Basic information

Entry
Database: PDB / ID: 2n29
TitleSolution-state NMR structure of Vpu cytoplasmic domain
ComponentsProtein Vpu
KeywordsVIRAL PROTEIN / alpha helix
Function / homology
Function and homology information


nuclear transport / uncoating of virus / RNA-templated DNA biosynthetic process / receptor catabolic process / Synthesis and processing of ENV and VPU / CD4 receptor binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / virion assembly / Minus-strand DNA synthesis ...nuclear transport / uncoating of virus / RNA-templated DNA biosynthetic process / receptor catabolic process / Synthesis and processing of ENV and VPU / CD4 receptor binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / virion assembly / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / host cell membrane / Binding and entry of HIV virion / monoatomic cation channel activity / viral life cycle / Vpu mediated degradation of CD4 / Assembly Of The HIV Virion / Budding and maturation of HIV virion / establishment of integrated proviral latency / suppression by virus of host tetherin activity / membrane => GO:0016020 / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / fusion of virus membrane with host plasma membrane / 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 / 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)6,2661
Polymers6,2661
Non-polymers00
Water0
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: 6265.957 Da / Num. of mol.: 1 / Fragment: cytoplasmic domain (UNP residues 28-81)
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: P05919*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D 15N/1N HSQC
1312D 15N/1N HSQCIPAP
2413D HNCA
2513D (H)CC(CO)NH
2613D CC(CO)NH
2713D 15N/13C'/13C
2813D HNCO
2913D HN(CA)CB

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Sample preparation

DetailsContents: 0.5 mM [U-100% 15N] Vpu Cytoplasmic domain, 0.5 mM [U-100% 13C; U-100% 15N] Vpu Cytoplasmic domain, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMVpu Cytoplasmic domain-1[U-100% 15N]1
0.5 mMVpu Cytoplasmic domain-2[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 5 / pH: 4.0 / Pressure: 1 atm / Temperature: 323 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 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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