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Yorodumi- PDB-1jaa: Solution structure of lactam analogue (DapE) of HIV gp41 600-612 loop. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jaa | ||||||
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Title | Solution structure of lactam analogue (DapE) of HIV gp41 600-612 loop. | ||||||
Components | DapE : (Ace)IWG(Dap)SGKLIETTA ANALOGUE OF HIV GP41 | ||||||
Keywords | VIRAL PROTEIN / lactam bond / cyclic peptide / peptidomimetics / gp41 / HIV | ||||||
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 / Torsion angle 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 | 1jaa.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jaa.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1jaa ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1jaa | HTTPS FTP |
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-Related structure data
Related structure data | 1im7C 1j8nC 1j8zC 1j9vC 1jarC 1jc8C 1jcpC 1jd8C 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: 1388.589 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The parent peptide (IWGCSGKLICTTA) occurs naturally in HIV gp41 glycoprotein References: UniProt: P12488 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using standard 2D homonuclear techniques. Different NOESY experiments , with mixing times from 80 ms to 800 ms , were recorded in order to determined the best ...Text: The structure was determined using standard 2D homonuclear techniques. Different NOESY experiments , with mixing times from 80 ms to 800 ms , were recorded in order to determined the best conditions avoiding spin diffusion. |
-Sample preparation
Details | Contents: 3 mM peptide in 500 ul DMSO-D6 / Solvent system: 100% DMSO-D6 |
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Sample conditions | Pressure: ambiant / Temperature: 298 K |
-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: Torsion angle dynamics, molecular dynamics, energy minimization. Software ordinal: 1 Details: 50 initial random structure were generatd in DYANA software , followed by 500 ps restrained minimization + 35 ps MD in vacuo at 300K, 200 ps under NMR restraints and 750ps conjugated ...Details: 50 initial random structure were generatd in DYANA software , followed by 500 ps restrained minimization + 35 ps MD in vacuo at 300K, 200 ps under NMR restraints and 750ps conjugated gradient EM using the DISCOVER module of MSI software | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 50 / Conformers submitted total number: 50 |