BMRB Entry 19666

Name: Structure of insect-specific sodium channel toxin mu-Dc1a
Published: 2014-07-14

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PDB ID: 2mi5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19666
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of insect-specific sodium channel toxin mu-Dc1a

Deposition date:

2013-12-08

Original release date:

2014-07-14

Authors:

Bende, Niraj; Mobli, Mehdi; King, Glenn

Citation:

Citation: Bende, Niraj; Dziemborowicz, Slawomir; Mobli, Mehdi; Herzig, Volker; Gilchrist, John; Nicholson, Graham; King, Glenn; Bosmans, Frank. "A distinct voltage-sensor locus determines insect-family selectivity of a unique sodium channel modulator found in desert bush spider venom" Nat. Commun. 5, 1-10 (2014).
PubMed: 25014760

Assembly members:

Assembly members:
Dc1a, polymer, 57 residues, 6502.466 Da.

Natural source:

Natural source: Common Name: desert bush spider Taxonomy ID: 38407 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Diguetia canities

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dc1a: SAKDGDVEGPAGCKKYDVEC DSGECCQKQYLWYKWRPLDC RCLKSGFFSSKCVCRDV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	245
15N chemical shifts	60
1H chemical shifts	374

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Dc1a	1

Entities:

Entity 1, Dc1a 57 residues - 6502.466 Da.

1

SER

ALA

LYS

ASP

GLY

ASP

VAL

GLU

GLY

PRO

2

ALA

GLY

CYS

LYS

TYR

ASP

VAL

GLU

CYS

3

ASP

SER

GLY

GLU

CYS

GLN

LYS

GLN

TYR

4

LEU

TRP

TYR

LYS

TRP

ARG

PRO

LEU

ASP

CYS

5

ARG

CYS

LEU

LYS

SER

GLY

PHE

SER

6

LYS

CYS

VAL

CYS

ARG

ASP

VAL

Samples:

sample_1: Dc1a, [U-99% 13C; U-99% 15N], 350 uM; sodium acetate 20 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.02 M; pH: 5.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
4D HCC(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3, Guntert, Mumenthaler and Wuthrich - structure solution

TALOS v+, Cornilescu, Delaglio and Bax - geometry optimization

XEASY, Bartels et al. - chemical shift assignment

TOPSPIN v3, Bruker Biospin - collection

Rowland_NMR_Toolkit v3, Jeffrey C. Hoch, Alan S. Stern - processing

GENPROC v2, Mehdi Mobli - processing

NMR spectrometers:

Bruker Avance 900 MHz

UNP	P49126
PDB	2MI5
GB	AAB60253
SP	P49126
AlphaFold	P49126 P49126