BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17430

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   Vector: Pet

Entity Sequences (FASTA):
Arenicin-2: RWCVYAYVRIRGVLVRYRRC W

Data sets:
Data typeCount
13C chemical shifts201
15N chemical shifts56
1H chemical shifts343

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Arenicin-2-11
2Arenicin-2-21

Entities:

Entity 1, Arenicin-2-1 21 residues - 2780.392 Da.

1   ARGTRPCYSVALTYRALATYRVALARGILE
2   ARGGLYVALLEUVALARGTYRARGARGCYS
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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_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

Related Database Links:

BMRB 15115
PDB
GB AAV65143
SP Q5SC59
AlphaFold Q5SC59

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts