BMRB Entry 17430

Name: Spatial structure of antimicrobial peptide Arenicin-2 dimer in DPC micelles
Published: 2011-06-07

Click here to enlarge.

PDB ID: 2l8x
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17430
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Spatial structure of antimicrobial peptide Arenicin-2 dimer in DPC micelles

Deposition date:

2011-01-27

Original release date:

2011-06-07

Authors:

Shenkarev, Zakhar; Trunov, Kirill; Paramonov, Alexander; Arseniev, Alexander

Citation:

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).
PubMed: 21627330

Assembly members:

Assembly members:
Arenicin-2, polymer, 21 residues, 2780.392 Da.

Natural source:

Natural source: Common Name: lugworm Taxonomy ID: 6344 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Arenicola marina

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: Pet

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	201
15N chemical shifts	56
1H chemical shifts	343

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

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

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

BMRB	15115
PDB	2JNI 2L8X
GB	AAV65143
SP	Q5SC59
AlphaFold	Q5SC59