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
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Title: Solution structure of the sodium channel toxin Hd1a PubMed: 25754331
Deposition date: 2014-06-01 Original release date: 2015-03-23
Authors: Klint, Julie; Mobli, Mehdi; King, Glenn
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).
Assembly members:
Hd1a, polymer, 36 residues, 3891.489 Da.
Natural source: Common Name: tarantula Taxonomy ID: 1046906 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Haplopelma doriae
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Hd1a: GACLGFGKSCNPSNDQCCKS
SSLACSTKHKWCKYEL
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 222 |
| 13C chemical shifts | 138 |
| 15N chemical shifts | 38 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | sodium channel toxin Hd1a | 1 |
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 | GLY | ALA | CYS | LEU | GLY | PHE | GLY | LYS | SER | CYS | ||||
| 2 | ASN | PRO | SER | ASN | ASP | GLN | CYS | CYS | LYS | SER | ||||
| 3 | SER | SER | LEU | ALA | CYS | SER | THR | LYS | HIS | LYS | ||||
| 4 | TRP | CYS | LYS | TYR | GLU | LEU |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | 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 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 4D HCC(CO)NH | sample_1 | isotropic | sample_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 simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts