+Open data
-Basic information
Entry | Database: PDB / ID: 2n28 | ||||||
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Title | Solid-state NMR structure of Vpu | ||||||
Components | Protein Vpu | ||||||
Keywords | VIRAL PROTEIN / alpha helix | ||||||
Function / homology | Function and homology information receptor catabolic process / CD4 receptor binding / host cell membrane / viral release from host cell / monoatomic cation channel activity / suppression by virus of host tetherin activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLID-STATE NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Zhang, H. / Lin, E.C. / Tian, Y. / Das, B.B. / Opella, S.J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n28.cif.gz | 35.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n28.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 2n28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/2n28 ftp://data.pdbj.org/pub/pdb/validation_reports/n2/2n28 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLID-STATE NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 8.5 mM [U-100% 13C; U-100% 15N] HIV-1 Virus protein U, 100% H2O Solvent system: 100%H2O |
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Sample | Conc.: 8.5 mM / Component: HIV-1 Virus protein U-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 20 / pH: 7.3 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software | Name: CNS / Developer: Brunger, A.T. et.al. / Classification: refinement |
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Refinement | Method: 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 representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 1 |