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Yorodumi- PDB-1jd8: Solution structure of lactam analogue DapD of HIV gp41 600-612 loop -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jd8 | |||||||||
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Title | Solution structure of lactam analogue DapD of HIV gp41 600-612 loop | |||||||||
Components | Transmembrane protein gp41Transmembrane protein | |||||||||
Keywords | VIRAL PROTEIN / cyclic peptide / gp41 / HIV / lactam bond / pseudopeptide | |||||||||
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 | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | SOLUTION NMR / torsion dynamics, molecular dynamics, energy minimization | |||||||||
Authors | Phan Chan Du, A. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein. Authors: Du, A.P. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jd8.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jd8.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jd8 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jd8 | HTTPS FTP |
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-Related structure data
Related structure data | 1im7C 1j8nC 1j8zC 1j9vC 1jaaC 1jarC 1jc8C 1jcpC 1jdkC C: citing same article (ref.) |
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Similar 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: 1373.556 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The parent peptide (IWGCSGKLICTTA) occurs naturally in HIV gp41 Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03377 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: Classical 2D homonuclear NMR technques were used. Different NOESY with different mixing time (from 80ms to 800ms) were recorded in order to determine the best conditions without spin diffusion. |
-Sample preparation
Details | Contents: 4mM peptide in 500 ul solvent / Solvent system: 100% DMSO-D6 |
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Sample conditions | Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion dynamics, molecular dynamics, energy minimization Software ordinal: 4 Details: 50 initial structures were generated using DYANA software, followed by 500 steps restrained minimization.Then using DISCOVER 3, 35 ps MD and 750 steps conjugate gradient EM. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |