BMRB Entry 19998

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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/BMR19998
MolProbity Validation Chart

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Title:
Solution structure of the sodium channel toxin Hd1a
Deposition date:
2014-06-01
Original release date:
2015-03-23
Authors:
Klint, Julie; Mobli, Mehdi; King, Glenn
Citation:

Citation: Klint, Julie; Vetter, Irina; Rupasinghe, Darshani; Er, Sing; Herzig, Volker; Mobli, Mehdi; Lewis, Richard; Bosmans, Frank; King, Glenn. "Seven novel modulators of the analgesic target Nav1.7 uncovered using a high-throughput venom-based discovery pipeline"  Br. J. Pharmacol. ., .-. (2015).
PubMed: 25754331

Assembly members:

Assembly members:
Hd1a, polymer, 36 residues, 3891.489 Da.

Natural source:

Natural source:   Common Name: tarantula   Taxonomy ID: 1046906   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Haplopelma doriae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pLic-MBP

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Hd1a: GACLGFGKSCNPSNDQCCKS SSLACSTKHKWCKYEL

Data sets:
Data typeCount
1H chemical shifts222
13C chemical shifts138
15N chemical shifts38

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1sodium channel toxin Hd1a1

Entities:

Entity 1, sodium channel toxin Hd1a 36 residues - 3891.489 Da.

The disulfide-bond connectivity is Cys3-Cys18, Cys10-Cys25, and Cys17-Cys32.

1   GLYALACYSLEUGLYPHEGLYLYSSERCYS
2   ASNPROSERASNASPGLNCYSCYSLYSSER
3   SERSERLEUALACYSSERTHRLYSHISLYS
4   TRPCYSLYSTYRGLULEU

Samples:

sample_1: Hd1a, [U-98% 13C; U-98% 15N], 0.5 mM; sodium acetate 20 mM; H2O 95%; D2O 5%

sample_conditions_1: temperature: 298 K; pH: 4.9; pressure: 1 atm; ionic strength: 20 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
4D HCC(CO)NHsample_1isotropicsample_conditions_1

Software:

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

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

TOPSPIN v3.1, Bruker Biospin - collection

Rowland_NMR_Toolkit v3, Stern, Mobli, Hoch - processing

XEASY, Bartels et al. - data analysis, chemical shift assignment

NMR spectrometers:

  • Bruker Avance 900 MHz

Related Database Links:

PDB

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