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Yorodumi- PDB-1niz: NMR structure of a V3 (MN isolate) peptide bound to 447-52D, a hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1niz | ||||||
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Title | NMR structure of a V3 (MN isolate) peptide bound to 447-52D, a human HIV-1 neutralizing antibody | ||||||
Components | Exterior membrane glycoprotein(GP120) | ||||||
Keywords | VIRAL PROTEIN / Peptide-Antibody complex / b-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 / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Sharon, M. / Kessler, N. / Levy, R. / Zolla-Pazner, S. / Gorlach, M. / Anglister, J. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Alternative Conformations of HIV-1 V3 Loops Mimic beta Hairpins in Chemokines, Suggesting a Mechanism for Coreceptor Selectivity. Authors: Sharon, M. / Kessler, N. / Levy, R. / Zolla-Pazner, S. / Gorlach, M. / Anglister, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1niz.cif.gz | 10.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1niz.ent.gz | 7.2 KB | Display | PDB format |
PDBx/mmJSON format | 1niz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/1niz ftp://data.pdbj.org/pub/pdb/validation_reports/ni/1niz | 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: 1907.270 Da / Num. of mol.: 1 / Fragment: V3 loop (residues 309-324) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: ENV / Plasmid: pet11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P05877 |
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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 triple-resonance NMR spectroscopy, in which the peptide was labeled while the antibody remained unlabeled. |
-Sample preparation
Details |
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Sample conditions |
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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 | Name: CNS / Version: 1.1 / Developer: Brunger / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: minimized average structure |
NMR ensemble | Conformers submitted total number: 1 |