BMRB Entry 17430
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17430
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Title: Spatial structure of antimicrobial peptide Arenicin-2 dimer in DPC micelles PubMed: 21627330
Deposition date: 2011-01-27 Original release date: 2011-06-07
Authors: Shenkarev, Zakhar; Trunov, Kirill; Paramonov, Alexander; Arseniev, Alexander
Citation: Shenkarev, Zakhar; Balandin, Sergey; Trunov, Kirill; Paramonov, Alexander; Sukhanov, Stanislav; Barsukov, Leonid; Arseniev, Alexander; Ovchinnikova, Tatiana. "Molecular mechanism of action of -hairpin antimicrobial peptide arenicin: oligomeric structure in dodecylphosphocholine micelles and pore formation in planar lipid bilayers." Biochemistry 50, 6255-6265 (2011).
Assembly members:
Arenicin-2, polymer, 21 residues, 2780.392 Da.
Natural source: Common Name: lugworm Taxonomy ID: 6344 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Arenicola marina
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Arenicin-2: RWCVYAYVRIRGVLVRYRRC
W
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 201 |
| 15N chemical shifts | 56 |
| 1H chemical shifts | 343 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Arenicin-2-1 | 1 |
| 2 | Arenicin-2-2 | 1 |
Entities:
Entity 1, Arenicin-2-1 21 residues - 2780.392 Da.
| 1 | ARG | TRP | CYS | VAL | TYR | ALA | TYR | VAL | ARG | ILE | ||||
| 2 | ARG | GLY | VAL | LEU | VAL | ARG | TYR | ARG | ARG | CYS | ||||
| 3 | TRP |
Samples:
sample_1: Arenicin-2, [U-100% 13C; U-100% 15N], 1.2 mM; Dodecil phosphocholine, [U-2H], 120 mM; D2O 100%
sample_2: Arenicin-2, [U-100% 15N], 1.2 mM; Dodecil phosphocholine, [U-2H], 120 mM; D2O 5%; H2O 95%
sample_3: Arenicin-2, [U-100% 13C; U-100% 15N], 1.2 mM; Dodecil phosphocholine, [U-2H], 120 mM; D2O 5%; H2O 95%
sample_conditions_1: pH: 4.5; pressure: 1 atm; temperature: 316 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_3 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_3 | isotropic | sample_conditions_1 |
Software:
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
CARA v1.8, Rochus Keller - chemical shift assignment, peak picking
TOPSPIN v2.1, Bruker Biospin - collection, processing
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts