BMRB Entry 31177
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31177
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Citation: Connelly, E.; Rintala-Dempsey, A.; Gundogdu, M.; Freeman, E.; Koszela, J.; Aguirre, J.; Zhu, G.; Kamarainen, O.; Tadayon, R.; Walden, H.; Shaw, G.. "Capturing the catalytic intermediates of parkin ubiquitination" Proc. Natl. Acad. Sci. U. S. A. 121, e2403114121-e2403114121 (2024).
PubMed: 39078678
Assembly members:
entity_1, polymer, 73 residues, 8280.427 Da.
entity_2, polymer, 75 residues, 8519.778 Da.
entity_ZN, non-polymer, 65.409 Da.
entity_4LJ, non-polymer, 138.006 Da.
Natural source: Common Name: fruit fly Taxonomy ID: 7227 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Drosophila melanogaster
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)
Entity Sequences (FASTA):
entity_1: TVDPNRAAEARWDEASNVTI
KVSTKPCPKCRTPTERDGGC
MHMVCTRAGCGFEWCWVCQT
EWTRDCMGAHWFG
entity_2: MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 230 |
| 15N chemical shifts | 117 |
| 1H chemical shifts | 117 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
| 3 | unit_3 | 3 |
| 4 | unit_4 | 3 |
| 5 | unit_5 | 4 |
Entities:
Entity 1, unit_1 73 residues - 8280.427 Da.
| 1 | THR | VAL | ASP | PRO | ASN | ARG | ALA | ALA | GLU | ALA | ||||
| 2 | ARG | TRP | ASP | GLU | ALA | SER | ASN | VAL | THR | ILE | ||||
| 3 | LYS | VAL | SER | THR | LYS | PRO | CYS | PRO | LYS | CYS | ||||
| 4 | ARG | THR | PRO | THR | GLU | ARG | ASP | GLY | GLY | CYS | ||||
| 5 | MET | HIS | MET | VAL | CYS | THR | ARG | ALA | GLY | CYS | ||||
| 6 | GLY | PHE | GLU | TRP | CYS | TRP | VAL | CYS | GLN | THR | ||||
| 7 | GLU | TRP | THR | ARG | ASP | CYS | MET | GLY | ALA | HIS | ||||
| 8 | TRP | PHE | GLY |
Entity 2, unit_2 75 residues - 8519.778 Da.
| 1 | MET | GLN | ILE | PHE | VAL | LYS | THR | LEU | THR | GLY | ||||
| 2 | LYS | THR | ILE | THR | LEU | GLU | VAL | GLU | PRO | SER | ||||
| 3 | ASP | THR | ILE | GLU | ASN | VAL | LYS | ALA | LYS | ILE | ||||
| 4 | GLN | ASP | LYS | GLU | GLY | ILE | PRO | PRO | ASP | GLN | ||||
| 5 | GLN | ARG | LEU | ILE | PHE | ALA | GLY | LYS | GLN | LEU | ||||
| 6 | GLU | ASP | GLY | ARG | THR | LEU | SER | ASP | TYR | ASN | ||||
| 7 | ILE | GLN | LYS | GLU | SER | THR | LEU | HIS | LEU | VAL | ||||
| 8 | LEU | ARG | LEU | ARG | GLY |
Entity 3, unit_3 - Zn - 65.409 Da.
| 1 | ZN |
Entity 4, unit_5 - C3 H8 Br N - 138.006 Da.
| 1 | 4LJ |
Samples:
sample_1: Rcat domain from Parkin, [U-13C; U-15N], 300 uM; Ubiquitin G75-C3 300 uM; NaCl 100 mM
sample_2: Rcat domain from Parkin, [U-13C; U-15N], 800 uM; Ubiquitin G75-C3 800 uM; NaCl 100 mM
sample_3: Rcat domain from Parkin 300 uM; Ubiquitin G75-C3, [U-13C; U-15N], 300 uM; NaCl 100 mM
sample_4: Rcat domain from Parkin, [U-13C; U-15N], 300 uM; NaCl 100 mM
sample_5: Ubiquitin G75-C3, [U-13C; U-15N], 500 uM; NaCl 100 mM
sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_3 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_4 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_5 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
Software:
NMRViewJ, Johnson and Blevins - chemical shift assignment
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation
HADDOCK, Bonvin - structure calculation
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMR spectrometers:
- Varian INOVA 600 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated peaks
SPARKY: Backbone
or all simulated peaks