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Yorodumi- PDB-2m8m: NMR assignment and structure of a peptide derived from the membra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m8m | ||||||
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Title | NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of hexafluoroisopropanol | ||||||
Components | Transmembrane protein gp41Transmembrane protein | ||||||
Keywords | VIRAL PROTEIN / HIV-1 gp41 protein / neutralizing epitope / peptide vaccine | ||||||
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 type 1 | ||||||
Method | SOLUTION NMR / torsion angle dynamics, molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Serrano, S. / Huarte, N. / Nieva, J.L. / Jimenez, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structure and Immunogenicity of a Peptide Vaccine, Including the Complete HIV-1 gp41 2F5 Epitope: IMPLICATIONS FOR ANTIBODY RECOGNITION MECHANISM AND IMMUNOGEN DESIGN. Authors: Serrano, S. / Araujo, A. / Apellaniz, B. / Bryson, S. / Carravilla, P. / de la Arada, I. / Huarte, N. / Rujas, E. / Pai, E.F. / Arrondo, J.L. / Domene, C. / Jimenez, M.A. / Nieva, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m8m.cif.gz | 196.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m8m.ent.gz | 166.7 KB | Display | PDB format |
PDBx/mmJSON format | 2m8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/2m8m ftp://data.pdbj.org/pub/pdb/validation_reports/m8/2m8m | 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: 3656.105 Da / Num. of mol.: 1 / Fragment: UNP residues 656-683 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P05878 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM MPERp, 67.5 % H2O, 7.5 % [U-100% 2H] D2O, 25 % hexafluoroisopropanol, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water Solvent system: hexafluoroisopropanol/water | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 2 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, molecular dynamics / Software ordinal: 1 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |