BMRB Entry 30696
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30696
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Title: Solution NMR structure of Dictyostelium discoideum Skp1A (truncated) dimer PubMed: 32227851
Deposition date: 2019-12-10 Original release date: 2020-04-13
Authors: Kim, H.; Eletsky, A.; West, C.
Citation: Kim, H.; Eletsky, A.; Gonzalez, K.; van der Wel, H.; Strauch, E.; Prestegard, J.; West, C.. "Skp1 Dimerization Conceals Its F-Box Protein Binding Site" Biochemistry 59, 1527-1536 (2020).
Assembly members:
entity_1, polymer, 116 residues, 12998.891 Da.
Natural source: Common Name: Slime mold Taxonomy ID: 44689 Superkingdom: Eukaryota Kingdom: not available Genus/species: Dictyostelium discoideum
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: SLVKLESSDEKVFEIEKEIA
CMSVTIKNMIEDIGESDSPI
PLPNVTSTILEKVLDYCRHH
HQHPGGSGLDDIPPYDRDFC
KVDQPTLFELILAANYLDIK
PLLDVTCKTVANMIRG
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 531 |
| 15N chemical shifts | 124 |
| 1H chemical shifts | 851 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1, 1 | 1 |
| 2 | entity_1, 2 | 1 |
Entities:
Entity 1, entity_1, 1 116 residues - 12998.891 Da.
| 1 | SER | LEU | VAL | LYS | LEU | GLU | SER | SER | ASP | GLU | ||||
| 2 | LYS | VAL | PHE | GLU | ILE | GLU | LYS | GLU | ILE | ALA | ||||
| 3 | CYS | MET | SER | VAL | THR | ILE | LYS | ASN | MET | ILE | ||||
| 4 | GLU | ASP | ILE | GLY | GLU | SER | ASP | SER | PRO | ILE | ||||
| 5 | PRO | LEU | PRO | ASN | VAL | THR | SER | THR | ILE | LEU | ||||
| 6 | GLU | LYS | VAL | LEU | ASP | TYR | CYS | ARG | HIS | HIS | ||||
| 7 | HIS | GLN | HIS | PRO | GLY | GLY | SER | GLY | LEU | ASP | ||||
| 8 | ASP | ILE | PRO | PRO | TYR | ASP | ARG | ASP | PHE | CYS | ||||
| 9 | LYS | VAL | ASP | GLN | PRO | THR | LEU | PHE | GLU | LEU | ||||
| 10 | ILE | LEU | ALA | ALA | ASN | TYR | LEU | ASP | ILE | LYS | ||||
| 11 | PRO | LEU | LEU | ASP | VAL | THR | CYS | LYS | THR | VAL | ||||
| 12 | ALA | ASN | MET | ILE | ARG | GLY |
Samples:
sample_1: DDSkp1, [U-90% 13C; U-90% 15N], 0.5 mM; MES 50 mM; NaCl 50 mM; DTT 5 mM; sodium azide 0.05%
sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 atm; temperature: 308 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D [15N, 1H]-HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D [13C, 1H] CT-HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D [13C, 1H] CT-HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C/15N-edited [1H,1H] NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D TROSY-HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CCH-COSY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CCH-COSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CCH-TOCSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 13C/15N-filtered 13C/15N-edited [1H,1H] NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D long-range [15N, 1H]-HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | 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 (HCA)CONH | sample_1 | isotropic | sample_conditions_1 |
Software:
TopSpin, Bruker Biospin - collection, processing
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CARA, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation
VNMR, Varian - collection
TALOS, Cornilescu, Delaglio and Bax - data analysis
PSVS, Bhattacharya and Montelione - data analysis
NMR spectrometers:
- Bruker AVANCE NEO 800 MHz
- Agilent VNMRS 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts