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- PDB-5nvp: NMR assignment and structure of a peptide derived from the fusion... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nvp | |||||||||
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Title | NMR assignment and structure of a peptide derived from the fusion peptide of HIV-1 gp41 in the presence of dodecylphosphocholine micelles | |||||||||
![]() | Envelope glycoprotein,Gp41 | |||||||||
![]() | VIRAL PROTEIN / Envelope glycoprotein gp41 / fusion peptide | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
![]() | Jimenez, M.A. / Serrano, S. / Nieva, J.L. / Huarte, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance. Authors: Serrano, S. / Huarte, N. / Rujas, E. / Andreu, D. / Nieva, J.L. / Jimenez, M.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249 KB | Display | ![]() |
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PDB format | ![]() | 210.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 383.7 KB | Display | ![]() |
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Full document | ![]() | 516.3 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nwuC ![]() 5nwvC ![]() 5nwwC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 3822.411 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Residues 1-15 are derived from gp41 fusion peptide and correspond to residues 514-528 of gp41. Residues 19-35 are derived from gp41 MPER region and correspond to residues 655-671 of gp41. ...Details: Residues 1-15 are derived from gp41 fusion peptide and correspond to residues 514-528 of gp41. Residues 19-35 are derived from gp41 MPER region and correspond to residues 655-671 of gp41. Residues 16-18 are the linker sequence. Source: (synth.) ![]() ![]() References: UniProt: A1YNH3, UniProt: Q69894, UniProt: P04578*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 | Type: micelle Contents: 0.6 mM wtFP-tag, 20 mM [U-98% 2H] DPC, 2.0 mM HEPES, 90 % H2O, 10 % [U-99% 2H] D2O, 0.1 mM DSS, 90% H2O/10% D2O Details: DPC micelles / Label: wtFP-tag / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 2 mM / Label: conditions_1 / pH: 6.8 pH* / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: equipped with a cryoprobe |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |