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Yorodumi- PDB-1pje: Structure of the channel-forming trans-membrane domain of Virus p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pje | ||||||
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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 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 / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLID-STATE NMR / Direct structural fitting of 2D solid-state NMR data | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pje.cif.gz | 11.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pje.ent.gz | 4.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pje_validation.pdf.gz | 249.4 KB | Display | wwPDB validaton report |
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Full document | 1pje_full_validation.pdf.gz | 249.1 KB | Display | |
Data in XML | 1pje_validation.xml.gz | 1.4 KB | Display | |
Data in CIF | 1pje_validation.cif.gz | 1.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pje ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pje | HTTPS FTP |
-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/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 |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR |
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NMR experiment | Type: PISEMA |
NMR details | Text: PISEMA: Polarization Inversion Spin Exchange at the Magic Angle |
-Sample preparation
Details | Contents: Completely aligned sample in glass plates: 3.5 mg Vpu2-30+ U-15N, 75 mg lipid mixture (DOPC:DOPG, 9:1) |
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Sample conditions | pH: 7.0 / Pressure: ambient / Temperature: 293 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
-Processing
NMR software |
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Refinement | Method: Direct structural fitting of 2D solid-state NMR data Software ordinal: 1 Details: This structure was calculated by using a structural fitting algorithm that finds torsion angles between consecutive residues based on their NMR frequencies | ||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||
NMR ensemble | Conformer selection criteria: minimized average structure / Conformers calculated total number: 100 / Conformers submitted total number: 1 |