BMRB Entry 30197
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30197
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Title: Solution structure of Serine 65 phosphorylated UBL domain from parkin PubMed: 28007983
Deposition date: 2016-10-25 Original release date: 2016-12-15
Authors: Aguirre, J.; Dunkerley, K.; Mercier, P.; Shaw, G.
Citation: Aguirre, J.; Dunkerley, K.; Mercier, P.; Shaw, G.. "Structure of phosphorylated parkin UBL domain and insights into PINK1-orchestrated activation" Proc. Natl. Acad. Sci. U.S.A. 114, 298-303 (2017).
Assembly members:
E3 ubiquitin-protein ligase parkin, polymer, 76 residues, 8916.063 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
E3 ubiquitin-protein ligase parkin: MIVFVRFNSSHGFPVEVDSD
TSIFQLKEVVAKRQGVPADQ
LRVIFAGKELRNDWTVQNCD
LDQQXIVHIVQRPWRK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 335 |
| 15N chemical shifts | 80 |
| 1H chemical shifts | 502 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 76 residues - 8916.063 Da.
| 1 | MET | ILE | VAL | PHE | VAL | ARG | PHE | ASN | SER | SER | ||||
| 2 | HIS | GLY | PHE | PRO | VAL | GLU | VAL | ASP | SER | ASP | ||||
| 3 | THR | SER | ILE | PHE | GLN | LEU | LYS | GLU | VAL | VAL | ||||
| 4 | ALA | LYS | ARG | GLN | GLY | VAL | PRO | ALA | ASP | GLN | ||||
| 5 | LEU | ARG | VAL | ILE | PHE | ALA | GLY | LYS | GLU | LEU | ||||
| 6 | ARG | ASN | ASP | TRP | THR | VAL | GLN | ASN | CYS | ASP | ||||
| 7 | LEU | ASP | GLN | GLN | SEP | ILE | VAL | HIS | ILE | VAL | ||||
| 8 | GLN | ARG | PRO | TRP | ARG | LYS |
Samples:
sample_2: DSS 200 uM; HEPES 25 mM; TCEP 250 uM; imidazole 300 uM; pUBL, [U-15N], 300 uM; sodium chloride 100 mM; H2O 90%; D2O 10%
sample_3: DSS 200 uM; HEPES 25 mM; TCEP 250 uM; imidazole 300 uM; pUBL, [U-13C], 300 uM; sodium chloride 100 mM; H2O 90%; D2O 10%
sample_4: DSS 200 uM; HEPES 25 mM; TCEP 250 uM; imidazole 300 uM; pUBL, [U-99% 13C; U-99% 15N], 400 uM; sodium chloride 100 mM; H2O 90%; D2O 10%
sample_5: DSS 200 uM; HEPES 25 mM; TCEP 250 uM; imidazole 300 uM; pUBL 400 uM; sodium chloride 100 mM; D2O 100%
sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_5 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_4 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_4 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_4 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_4 | isotropic | sample_conditions_1 |
| 2D (HB)CB(CGCD)HD | sample_5 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_4 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_5 | isotropic | sample_conditions_1 |
Software:
CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation
NMRPipe v8.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView v8.2.4, Johnson, One Moon Scientific - data analysis
VNMR v3.2, Varian - collection
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMR spectrometers:
- Varian INOVA 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts