BMRB Entry 19783
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19783
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Title: Solution structure of the fourth constant immunoglobulin domain of nurse shark IgNAR PubMed: 24830426
Deposition date: 2014-02-10 Original release date: 2014-06-30
Authors: Hennig, Janosch; Sattler, Michael
Citation: Feige, Matthias; Griwert, Melissa; Marcinowski, Moritz; Hennig, Janosch; Behnke, Julia; Auslinder, David; Herold, Eva; Peschek, Jirka; Castro, Caitlin; Flajnik, Martin; Hendershot, Linda; Sattler, Michael; Groll, Michael; Buchner, Johannes. "The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins" Proc. Natl. Acad. Sci. U.S.A. 111, 8155-8160 (2014).
Assembly members:
entity, polymer, 105 residues, 11832.534 Da.
Natural source: Common Name: Nurse shark Taxonomy ID: 7801 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Ginglymostoma cirratum
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: MGRQTDISVSLLKPPFEEIW
TQQTATIVCEIVYSDLENIK
VFWQVNGVERKKGVETQNPE
WSGSKSTIVSKLKVMASEWD
SGTEYVCLVEDSELPTPVKA
SIRKA
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 394 |
| 15N chemical shifts | 97 |
| 1H chemical shifts | 704 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Fourth counstant immunoglobulin domain of IgNAR | 1 |
Entities:
Entity 1, Fourth counstant immunoglobulin domain of IgNAR 105 residues - 11832.534 Da.
| 1 | MET | GLY | ARG | GLN | THR | ASP | ILE | SER | VAL | SER | ||||
| 2 | LEU | LEU | LYS | PRO | PRO | PHE | GLU | GLU | ILE | TRP | ||||
| 3 | THR | GLN | GLN | THR | ALA | THR | ILE | VAL | CYS | GLU | ||||
| 4 | ILE | VAL | TYR | SER | ASP | LEU | GLU | ASN | ILE | LYS | ||||
| 5 | VAL | PHE | TRP | GLN | VAL | ASN | GLY | VAL | GLU | ARG | ||||
| 6 | LYS | LYS | GLY | VAL | GLU | THR | GLN | ASN | PRO | GLU | ||||
| 7 | TRP | SER | GLY | SER | LYS | SER | THR | ILE | VAL | SER | ||||
| 8 | LYS | LEU | LYS | VAL | MET | ALA | SER | GLU | TRP | ASP | ||||
| 9 | SER | GLY | THR | GLU | TYR | VAL | CYS | LEU | VAL | GLU | ||||
| 10 | ASP | SER | GLU | LEU | PRO | THR | PRO | VAL | LYS | ALA | ||||
| 11 | SER | ILE | ARG | LYS | ALA |
Samples:
sample_1: Fourth counstant immunoglobulin domain of IgNAR, [U-100% 13C; U-100% 15N], 300 – 500 uM; sodium chloride 137 mM; potassium chloride 2.7 mM; sodium phosphate 10 mM; potassium phosphate 2 mM; sodium azide 0.02%; H2O 90%; D2O 10%
sample_2: Fourth counstant immunoglobulin domain of IgNAR, [U-10% 13C], 300 – 500 uM; sodium chloride 137 mM; potassium chloride 2.7 mM; sodium phosphate 10 mM; potassium phosphate 2 mM; sodium azide 0.02%; sodium azide 90%; sodium azide 10%
sample_3: Fourth counstant immunoglobulin domain of IgNAR, [U-100% 13C; U-100% 15N], 300 – 500 uM; sodium chloride 137 mM; potassium chloride 2.7 mM; sodium phosphate 10 mM; potassium phosphate 2 mM; sodium azide 0.02%; Pf1 phage 10 mg/mL; H2O 90%; D2O 10%
sample_conditions_1: pH: 7.4; 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 aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | 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 HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | 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 |
| 2D 1H-13C HSQC aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_3 | isotropic | sample_conditions_1 |
Software:
CARA, Keller and Wuthrich - chemical shift assignment, peak picking
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure calculation
ARIA, Linge, O, . - water refinement
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 750 MHz
- Bruker Avance 800 MHz
- 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