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- PDB-1jau: NMR Solution Structure of the Trp-Rich Peptide of HIV gp41 Bound ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jau | ||||||
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Title | NMR Solution Structure of the Trp-Rich Peptide of HIV gp41 Bound to DPC Micelles | ||||||
![]() | TRANSMEMBRANE GLYCOPROTEIN (GP41) | ||||||
![]() | VIRAL PROTEIN / amphipathic alpha helix | ||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation | ||||||
![]() | Schibli, D.J. / Montelaro, R.C. / Vogel, H.J. | ||||||
![]() | ![]() Title: The membrane-proximal tryptophan-rich region of the HIV glycoprotein, gp41, forms a well-defined helix in dodecylphosphocholine micelles. Authors: Schibli, D.J. / Montelaro, R.C. / Vogel, H.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 | ![]() | 251.7 KB | Display | ![]() |
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PDB format | ![]() | 202.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 335.5 KB | Display | ![]() |
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Full document | ![]() | 515.4 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 21.7 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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1 |
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 2569.979 Da / Num. of mol.: 1 / Fragment: residues 665-683 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Human Immunodeficiency Virus (HIV). References: UniProt: P04624 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 200 mM DPC-d38 / pH: 3.51 / Pressure: ambient / Temperature: 310 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 |
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Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, molecular dynamics, matrix relaxation Software ordinal: 1 Details: Structures were initially generated using CNS. Ambiguous and unassigned noe constraints were then used in conjuction with matrix relaxation analysis using the program ARIA. | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 40 |