BMRB Entry 34167
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34167
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Title: Solution structure of domain III (DIII)of Zika virus Envelope protein PubMed: 28938115
Deposition date: 2017-08-02 Original release date: 2017-09-29
Authors: Zerbe, O.; Bardelli, M.
Citation: Wang, J.; Bardelli, M.; Espinosa, D.; Pedotti, M.; Ng, T.; Bianchi, S.; Simonelli, L.; Lim, E.; Foglierini, M.; Zatta, F.; Jaconi, S.; Beltramello, M.; Cameroni, E.; Fibriansah, G.; Shi, J.; Barca, T.; Pagani, I.; Rubio, A.; Broccoli, V.; Vicenzi, E.; Graham, V.; Pullan, S.; Dowall, S.; Hewson, R.; Jurt, S.; Zerbe, O.; Stettler, K.; Lanzavecchia, A.; Sallusto, F.; Cavalli, A.; Harris, E.; Lok, S.; Varani, L.; Corti, D.. "A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential." Cell 171, 229-241.e15 (2017).
Assembly members:
entity_1, polymer, 115 residues, 12479.393 Da.
Natural source: Common Name: ZIKV Taxonomy ID: 64320 Superkingdom: Viruses Kingdom: not available Genus/species: Flavivirus Zika virus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: MDKLRLKGVSYSLCTAAFTF
TKIPAETLHGTVTVEVQYAG
TDGPCKVPAQMAVDMQTLTP
VGRLITANPVITESTENSKM
MLELDPPFGDSYIVIGVGEK
KITHHWHRSGSTIGK
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 474 |
| 15N chemical shifts | 110 |
| 1H chemical shifts | 721 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 115 residues - 12479.393 Da.
| 1 | MET | ASP | LYS | LEU | ARG | LEU | LYS | GLY | VAL | SER | ||||
| 2 | TYR | SER | LEU | CYS | THR | ALA | ALA | PHE | THR | PHE | ||||
| 3 | THR | LYS | ILE | PRO | ALA | GLU | THR | LEU | HIS | GLY | ||||
| 4 | THR | VAL | THR | VAL | GLU | VAL | GLN | TYR | ALA | GLY | ||||
| 5 | THR | ASP | GLY | PRO | CYS | LYS | VAL | PRO | ALA | GLN | ||||
| 6 | MET | ALA | VAL | ASP | MET | GLN | THR | LEU | THR | PRO | ||||
| 7 | VAL | GLY | ARG | LEU | ILE | THR | ALA | ASN | PRO | VAL | ||||
| 8 | ILE | THR | GLU | SER | THR | GLU | ASN | SER | LYS | MET | ||||
| 9 | MET | LEU | GLU | LEU | ASP | PRO | PRO | PHE | GLY | ASP | ||||
| 10 | SER | TYR | ILE | VAL | ILE | GLY | VAL | GLY | GLU | LYS | ||||
| 11 | LYS | ILE | THR | HIS | HIS | TRP | HIS | ARG | SER | GLY | ||||
| 12 | SER | THR | ILE | GLY | LYS |
Samples:
sample_1: ZIKA Envelope DIII, [U-15N; U-13C], 800 uM; sodium chloride 50 mM; sodium phosphate 20 mM
sample_2: ZIKA Envelope DIII, [U-2H; U-15N; U-13C], 400 ± 10 uM; ZKA190 Fab 440 ± 10 uM; sodium chloride 50 ± 1 mM; sodium phosphate 20 ± 1 mM
sample_conditions_1: ionic strength: 0.27 mM; pH: 6.0; pressure: 1 atm; temperature: 300 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | 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 HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D H(C)CH | 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 |
Software:
CARA v1.93, Keller and Wuthrich - chemical shift assignment
CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation
TOPSPIN v2.1, Bruker Biospin - processing
NMR spectrometers:
- Bruker AV-4 600 MHz
- Bruker Avance 700 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts