BMRB Entry 19583
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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/BMR19583
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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 dodecylphosphocholine micelles
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:
CpreTM, polymer, 28 residues, 3489.345 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):
CpreTM: KKKNWFDITNWLWYIKLFIM
IVGGLVKK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 20 |
| 1H chemical shifts | 243 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | CpreTM | 1 |
Entities:
Entity 1, CpreTM 28 residues - 3489.345 Da.
The sequence NWFDITNWLWYIKLFIMIVGGLVK corresponds to residues 656-683 of glycoprotein gp41 from HIV. The three N-terminal residues (KKK) and the C-terminal K were added to the native sequence to improve peptide solubility.
| 1 | LYS | LYS | LYS | ASN | TRP | PHE | ASP | ILE | THR | ASN | ||||
| 2 | TRP | LEU | TRP | TYR | ILE | LYS | LEU | PHE | ILE | MET | ||||
| 3 | ILE | VAL | GLY | GLY | LEU | VAL | LYS | LYS |
Samples:
sample_1: CpreTM 0.5 mM; H2O 90%; D2O, [U-100% 2H], 10%; DPC, [U-99% 2H], 20 mM; 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