BMRB Entry 27977
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27977
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Title: Solution structure of the PUB domain of human UBXD1 protein
Deposition date: 2019-07-17 Original release date: 2019-12-17
Authors: Beuck, Christine; Bayer, Peter; Blueggel, Mike
Citation: Blueggel, Mike; van den Boom, Johannes; Meyer, Hemmo; Bayer, Peter; Beuck, Christine. "Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase" Biomolecules 9, 876-876 (2019).
Assembly members:
UBXD1-PUB_domain, polymer, 119 residues, 13804 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):
UBXD1-PUB_domain: GSHMSTDPVAASIMKIYTFN
KDQDRVKLGVDTIAKYLDNI
HLHPEEEKYRKIKLQNKVFQ
ERINCLEGTHEFFEAIGFQK
VLLPAQDQEDPEEFYVLSET
TLAQPQSLERHKEQLLAAE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 535 |
| 15N chemical shifts | 117 |
| 1H chemical shifts | 811 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | UBXD1-PUB domain | 1 |
Entities:
Entity 1, UBXD1-PUB domain 119 residues - 13804 Da.
Residues -4 to -1 represent a cloning artifact
| 1 | GLY | SER | HIS | MET | SER | THR | ASP | PRO | VAL | ALA | ||||
| 2 | ALA | SER | ILE | MET | LYS | ILE | TYR | THR | PHE | ASN | ||||
| 3 | LYS | ASP | GLN | ASP | ARG | VAL | LYS | LEU | GLY | VAL | ||||
| 4 | ASP | THR | ILE | ALA | LYS | TYR | LEU | ASP | ASN | ILE | ||||
| 5 | HIS | LEU | HIS | PRO | GLU | GLU | GLU | LYS | TYR | ARG | ||||
| 6 | LYS | ILE | LYS | LEU | GLN | ASN | LYS | VAL | PHE | GLN | ||||
| 7 | GLU | ARG | ILE | ASN | CYS | LEU | GLU | GLY | THR | HIS | ||||
| 8 | GLU | PHE | PHE | GLU | ALA | ILE | GLY | PHE | GLN | LYS | ||||
| 9 | VAL | LEU | LEU | PRO | ALA | GLN | ASP | GLN | GLU | ASP | ||||
| 10 | PRO | GLU | GLU | PHE | TYR | VAL | LEU | SER | GLU | THR | ||||
| 11 | THR | LEU | ALA | GLN | PRO | GLN | SER | LEU | GLU | ARG | ||||
| 12 | HIS | LYS | GLU | GLN | LEU | LEU | ALA | ALA | GLU |
Samples:
sample_1: UBXD1-PUB domain, [U-98% 13C; U-98% 15N], 600-900 uM; potassium phosphate 16 mM; sodium phosphate 34 mM; H2O 90%; D2O, [U-2H], 10%; DSS 0.1 mM
sample_2: UBXD1-PUB domain, [U-98% 13C; U-98% 15N], 500 uM; potassium phosphate 16 mM; sodium phosphate 34 mM; D2O, [U-99% 2H], 100%; DSS 0.1 mM
sample_3: UBXD1-PUB domain, [U-98% 15N], 700 uM; potassium phosphate 16 mM; sodium phosphate 34 mM; H2O 90%; D2O, [U-2H], 10%; DSS 0.1 mM
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | 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 HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D HC(C)H-COSY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HC(C)H-TOCSY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HC(C)H-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D Histidin H(C)N-SOFAST-HMQC | sample_1 | isotropic | sample_conditions_1 |
Software:
TOPSPIN vV. 3.5, Bruker Biospin - collection, processing
CARA v1.6, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking
UNIO v10, Herrmann - NOE assignment, NOESY peak picking
CYANA v3.98.9, Guntert, Mumenthaler and Wuthrich - structure solution
YASARA v11.12.31, Krieger - refinement
NMR spectrometers:
- 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