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Yorodumi- PDB-1u6v: NMR structure of a V3 (IIIB isolate) peptide bound to 447-52D, a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u6v | ||||||
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Title | NMR structure of a V3 (IIIB isolate) peptide bound to 447-52D, a human HIV-1 neutralizing antibody | ||||||
Components | V3 peptide | ||||||
Keywords | VIRAL PROTEIN / Beta hairpin | ||||||
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 / distance geometry, simulated annealing | ||||||
Authors | Rosen, O. / Chill, J. / Sharon, M. / Kessler, N. / Mester, B. / Zolla-Pazner, S. / Anglister, J. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Induced fit in HIV-neutralizing antibody complexes: evidence for alternative conformations of the gp120 V3 loop and the molecular basis for broad neutralization. Authors: Rosen, O. / Chill, J. / Sharon, M. / Kessler, N. / Mester, B. / Zolla-Pazner, S. / Anglister, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u6v.cif.gz | 142.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u6v.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 1u6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/1u6v ftp://data.pdbj.org/pub/pdb/validation_reports/u6/1u6v | 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: 1860.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: IIIB isolate / Plasmid: pM4-V3IIIB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS / References: UniProt: P03377*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 10mM acetic acid / pH: 5 / Pressure: ambient / Temperature: 305 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: distance geometry, simulated annealing / Software ordinal: 1 Details: The structure is based on 370 restraints, 21 dihedral angles and 5 hydrogen bonds | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 30 |