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- PDB-2gof: Three-dimensional structure of the trans-membrane domain of Vpu f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gof | ||||||
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Title | Three-dimensional structure of the trans-membrane domain of Vpu from HIV-1 in aligned phospholipid bicelles | ||||||
![]() | VPU protein | ||||||
![]() | VIRAL PROTEIN / single trans-membrane helix / bicelle / magnetic alignment | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | SOLUTION NMR / Structural fitting | ||||||
Model type details | minimized average | ||||||
![]() | Park, S.H. / De Angelis, A.A. / Nevzorov, A.A. / Wu, C.H. / Opella, S.J. | ||||||
![]() | ![]() Title: Three-Dimensional Structure of the Transmembrane Domain of Vpu from HIV-1 in Aligned Phospholipid Bicelles. Authors: Park, S.H. / De Angelis, A.A. / Nevzorov, A.A. / Wu, C.H. / Opella, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.1 KB | Display | ![]() |
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PDB format | ![]() | 24.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 324.3 KB | Display | ![]() |
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Full document | ![]() | 403.6 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 3742.689 Da / Num. of mol.: 1 / Fragment: Trans-membrane domain, residues 2-30 / Mutation: Y29G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: PISEMA |
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Sample preparation
Details | Type: bicelle Contents: 15N-uniformly or selectively peptide aligned in 16C bicelles (1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (14-O-PC) / 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (6-O-PC) = 3.0, 28% w/v), 100% H2O Label: sample_1 / Solvent system: 100% H2O |
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Sample conditions | Temperature: 313 K |
-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: 900 MHz |
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Processing
NMR software | Name: Structural Fitting / Developer: Nevzorov, A.A. et al. / Classification: refinement |
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Refinement | Method: Structural fitting / Software ordinal: 1 Details: Orientational frequencies (15N chemical shift and 15N-1H dipolar coupling) for each amide site were used. |
NMR representative | Selection criteria: minimized average structure |
NMR ensemble | Conformer selection criteria: first 20 structures / Conformers calculated total number: 100 / Conformers submitted total number: 21 |