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Yorodumi- PDB-1jav: AVERAGE NMR SOLUTION STRUCTURE OF THE TRP-RICH PEPTIDE OF HIV GP4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jav | ||||||
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Title | AVERAGE NMR SOLUTION STRUCTURE OF THE TRP-RICH PEPTIDE OF HIV GP41 BOUND TO DPC MICELLES | ||||||
Components | TRANSMEMBRANE GLYCOPROTEIN (GP41) | ||||||
Keywords | VIRAL PROTEIN / amphipathic alpha helix | ||||||
Function / homology | Function and homology information Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane Similarity search - Function | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation | ||||||
Authors | Schibli, D.J. / Montelaro, R.C. / Vogel, H.J. | ||||||
Citation | Journal: Biochemistry / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jav.cif.gz | 13.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jav.ent.gz | 9.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1jav ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1jav | 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/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. |
-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 | Conformers submitted total number: 1 |