[English] 日本語
Yorodumi- PDB-1pi8: Structure of the channel-forming trans-membrane domain of Virus p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pi8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the channel-forming trans-membrane domain of Virus protein "u" (Vpu) from HIV-1 | ||||||
Components | VPU protein | ||||||
Keywords | VIRAL PROTEIN / ALPHA HELIX | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLID-STATE NMR / SCWRL 2.1 | ||||||
Authors | Park, S.H. / Mrse, A.A. / Nevzorov, A.A. / Mesleh, M.F. / Oblatt-Montal, M. / Montal, M. / Opella, S.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1 Authors: Park, S.H. / Mrse, A.A. / Nevzorov, A.A. / Mesleh, M.F. / Oblatt-Montal, M. / Montal, M. / Opella, S.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pi8.cif.gz | 28.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pi8.ent.gz | 16.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pi8_validation.pdf.gz | 342.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1pi8_full_validation.pdf.gz | 352.1 KB | Display | |
Data in XML | 1pi8_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 1pi8_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/1pi8 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/1pi8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 3873.885 Da / Num. of mol.: 1 / Fragment: Trans-membrane domain / Mutation: Y29G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: VPU / Plasmid: pET-31b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS / References: UniProt: Q70625 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR |
---|---|
NMR experiment | Type: PISEMA |
NMR details | Text: PISEMA: Polarization Inversion Spin Exchange at the Magic Angle |
-Sample preparation
Details | Contents: Completely aligned in glass plates: 3.5 mg Vpu2-30+ U-15N, 75 mg lipid mixture (DOPC:DOPG, 9:1) Solvent system: NA |
---|---|
Sample conditions | pH: 7 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
---|---|
Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: SCWRL 2.1 / Software ordinal: 1 Details: This structure was constructed as a symmetric tetramer of the Vpu2-30+ trans-membrane construct based on the empirical minimization of energy upon the addition of sidechains to a backbone ...Details: This structure was constructed as a symmetric tetramer of the Vpu2-30+ trans-membrane construct based on the empirical minimization of energy upon the addition of sidechains to a backbone structure that was generated from solid-state NMR data using the program SCWRL. | ||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||
NMR ensemble | Conformers submitted total number: 4 |