BMRB Entry 19581
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19581
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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
Deposition date: 2013-10-24 Original release date: 2015-03-23
Authors: Serrano, Soraya; Apellaniz, Beatriz; Huarte, Nerea; Nieva, Jose; Jimenez, M. Angeles
Citation: Serrano, Soraya; Apellaniz, Beatriz; Huarte, Nerea; Jimenez, M. Angeles; Nieva, Jose. "The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and its Connection to the Inmmunogenic Membrane-proximal External Region" Not known ., .-..
Assembly members:
TMDp, polymer, 27 residues, 3006.957 Da.
Natural source: Common Name: HIV Taxonomy ID: 12721 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human immunodeficiency virus
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
TMDp: KKKLFIMIVGGLVGLRIVFA
VLSIKKK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 94 |
| 1H chemical shifts | 231 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | peptide derived from the trans-membrane region of HIV-1 gp41 | 1 |
Entities:
Entity 1, peptide derived from the trans-membrane region of HIV-1 gp41 27 residues - 3006.957 Da.
Residues KLFIMIVGGLVGLRIVFAVLSI correspond to residues 683-704 of glycoprotein gp41 from HIV. The two N-terminal residues (KK) and the three C-terminal residues (KKK) were added to increase peptide solubility.
| 1 | LYS | LYS | LYS | LEU | PHE | ILE | MET | ILE | VAL | GLY | ||||
| 2 | GLY | LEU | VAL | GLY | LEU | ARG | ILE | VAL | PHE | ALA | ||||
| 3 | VAL | LEU | SER | ILE | LYS | LYS | LYS |
Samples:
sample_1: TMDp 0.5 mM; H2O 67.5%; D2O, [U-100% 2H], 7.5%; hexafluoroisopropanol 25%; HEPES 2 mM; DSS 0.1 mM
sample_conditions_1: ionic strength: 2 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
Software:
TOPSPIN, Bruker Biospin - collection, processing
SPARKY, Goddard - chemical shift assignment
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
NMR spectrometers:
- Bruker Avance 600 MHz