BMRB Entry 25071
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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/BMR25071
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Title: NMR structure of the ubiquitin-binding zinc finger (UBZ) domain from human Rad18 PubMed: 25162118
Deposition date: 2014-07-03 Original release date: 2014-09-19
Authors: Rizzo, Alessandro; Salerno, Paige; Bezsonova, Irina; Korzhnev, Dmitry
Citation: Rizzo, Alessandro; Salerno, Paige; Bezsonova, Irina; Korzhnev, Dmitry. "NMR Structure of the Human Rad18 Zinc Finger in Complex with Ubiquitin Defines a Class of UBZ Domains in Proteins Linked to the DNA Damage Response." Biochemistry 53, 5895-5906 (2014).
Assembly members:
Rad18-UBZ, polymer, 33 residues, 3628.145 Da.
ZINC ION, non-polymer, 65.409 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):
Rad18-UBZ: GSRQVTKVDCPVCGVNIPES
HINKHLDSCLSRE
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 1H chemical shifts | 168 |
| 13C chemical shifts | 102 |
| 15N chemical shifts | 27 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Rad18-UBZ | 1 |
| 2 | ZINC ION | 2 |
Entities:
Entity 1, Rad18-UBZ 33 residues - 3628.145 Da.
| 1 | GLY | SER | ARG | GLN | VAL | THR | LYS | VAL | ASP | CYS | ||||
| 2 | PRO | VAL | CYS | GLY | VAL | ASN | ILE | PRO | GLU | SER | ||||
| 3 | HIS | ILE | ASN | LYS | HIS | LEU | ASP | SER | CYS | LEU | ||||
| 4 | SER | ARG | GLU |
Entity 2, ZINC ION - Zn - 65.409 Da.
| 1 | ZN |
Samples:
Rad18_UBZ_sample: Rad18_UBZ, [U-13C; U-15N], 0.5 – 1.5 mM; MOPS-NaOH 25 mM; NaCl 50 mM; ZnCl2 0.05 mM; H2O 90%; D2O 10%
MOPS_NMR_buffer: temperature: 273 K; pH: 6.5; pressure: 1 atm; ionic strength: 150 mM
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
| 3D HNCO | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
| 3D HNCACB | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
| 3D HCCH-TOCSY | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
| 3D HBHA(CO)NH | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
| 3D 1H-15N NOESY | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
| 3D 1H-13C NOESY | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
| 3D CBCA(CO)NH | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
| 3D CCH-TOCSY | Rad18_UBZ_sample | isotropic | MOPS_NMR_buffer |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
CCPNmr_Analysis, CCPN - chemical shift assignment
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
NMR spectrometers:
- Varian VNMRS 800 MHz
- Varian VNMRS 600 MHz
- Varian VNMRS 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts