+Open data
-Basic information
Entry | Database: PDB / ID: 1mzi | ||||||
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Title | Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope | ||||||
Components | 2F5 epitope of HIV-1 gp41 fusion protein | ||||||
Keywords | VIRAL PROTEIN / Ensemble / statistics | ||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / 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 ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / 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 / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 / Ensemble generation with MEDUSA, Clustering analysis with NMRCLUST, Statistical analysis of the ensemble with NAMFIS | ||||||
Authors | Barbato, G. / Bianchi, E. / Ingallinella, P. / Hurni, W.H. / Miller, M.D. / Ciliberto, G. / Cortese, R. / Bazzo, R. / Shiver, J.W. / Pessi, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural analysis of the epitope of the anti-HIV antibody 2F5 sheds light into its mechanism of neutralization and HIV fusion. Authors: Barbato, G. / Bianchi, E. / Ingallinella, P. / Hurni, W.H. / Miller, M.D. / Ciliberto, G. / Cortese, R. / Bazzo, R. / Shiver, J.W. / Pessi, A. #1: Journal: J.Biomol.NMR / Year: 1991 Title: Multi-conformational peptide dynamics derived from NMR data: a new search algorithm and its application to antamanide Authors: Bruschweiler, R. / Blackledge, M. / Ernst, R.R. #2: Journal: J.Am.Chem.Soc. / Year: 1995 Title: NMR analysis of molecular flexibility in solution: a new method for the study of complex distributions of rapidly exchanging conformations. Application to a 13-residue peptide with an 8-residue loop Authors: Cicero, D.O. / Barbato, G. / Bazzo, R. #3: Journal: Protein Eng. / Year: 1996 Title: An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies Authors: Kelley, L.A. / Gardner, S.P. / Sutcliffe, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mzi.cif.gz | 326.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mzi.ent.gz | 247.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/1mzi ftp://data.pdbj.org/pub/pdb/validation_reports/mz/1mzi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1617.820 Da / Num. of mol.: 1 / Fragment: 13 residues 2F5 epitope / Source method: obtained synthetically / Details: GP160 HIV-1 HBX2 isolate amino acids 659-671 / References: UniProt: P04578 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Distance restraints were determined using NOESY build-up curves. The coupling constants were determined using phase sensitive COSY and TOCSY experiments. E threshold cutoff and deltaE allowance ...Text: Distance restraints were determined using NOESY build-up curves. The coupling constants were determined using phase sensitive COSY and TOCSY experiments. E threshold cutoff and deltaE allowance for MEDUSA were 600 and 100 kCal/mol respectively Clustering was performed with a cutoff of 1.0Angstrom A conformer was defined as different if either phi or psi angle for at least one aminoacid was differing by >15 degrees |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 50mM phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 278 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: Ensemble generation with MEDUSA, Clustering analysis with NMRCLUST, Statistical analysis of the ensemble with NAMFIS Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Base set ensemble representative of the conformational space experimentally allowed Conformers calculated total number: 6400 / Conformers submitted total number: 81 |