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Yorodumi- PDB-2mg1: NMR assignment and structure of a peptide derived from the trans-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mg1 | ||||||
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Title | NMR assignment and structure of a peptide derived from the trans-membrane region of HIV-1 gp41 in the presence of hexafluoroisopropanol | ||||||
Components | Transmembrane protein gp41 | ||||||
Keywords | VIRAL PROTEIN / HIV-1 gp41 protein / transmembrane domain / VIRAL ENTRY / MEMBRANE FUSION GLYCOPROTEIN | ||||||
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 / host cell endosome membrane / actin filament organization ...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 / 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 / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / torsion angle dynamics, molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Serrano, S. / Apellaniz, B. / Huarte, N.L. / Nieva, J.L. / Jimenez, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region. Authors: Apellaniz, B. / Rujas, E. / Serrano, S. / Morante, K. / Tsumoto, K. / Caaveiro, J.M. / 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 | 2mg1.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mg1.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 2mg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mg1_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 2mg1_full_validation.pdf.gz | 520.9 KB | Display | |
Data in XML | 2mg1_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2mg1_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/2mg1 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/2mg1 | HTTPS FTP |
-Related structure data
Related structure data | 2mg2C 2mg3C 4wy7C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3006.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578 |
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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 TMDp, 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 |