BMRB Entry 16390
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16390
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Title: NMR solution structure of human ubiquitin-like domain of ubiquilin 1, Northeast Structural Genomics Consortium (NESG) target HT5A
Deposition date: 2009-06-30 Original release date: 2009-07-07
Authors: Doherty, Ryan; Dhe-Paganon, Sirano; Fares, Christophe; Lemak, Sasha; Gutmanas, Aleks; Garcia, Maite; Yee, Adelinda; Montelione, Gaetano; Arrowsmith, Cheryl
Citation: Doherty, Ryan; Dhe-Paganon, Sirano; Fares, Christophe; Lemak, Sasha; Gutmanas, Aleks; Garcia, Maite; Yee, Adelinda; Montelione, Gaetano; Arrowsmith, Cheryl. "Solution structure of ubiquitin-like domain of ubiquilin 1." Not known ., .-..
Assembly members:
ubiquilin_1, polymer, 101 residues, 9053.559 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):
ubiquilin_1: MGSSHHHHHHSSGRENLYFQ
GHPKIMKVTVKTPKEKEEFA
VPENSSVQQFKEEISKRFKS
HTDQLVLIFAGKILKDQDTL
SQHGIHDGLTVHLVIKTQNR
P
- assigned_chemical_shifts
- RDCs
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 328 |
| 15N chemical shifts | 79 |
| 1H chemical shifts | 545 |
| residual dipolar couplings | 75 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | ubiquilin_1 | 1 |
Entities:
Entity 1, ubiquilin_1 101 residues - 9053.559 Da.
| 1 | MET | GLY | SER | SER | HIS | HIS | HIS | HIS | HIS | HIS | ||||
| 2 | SER | SER | GLY | ARG | GLU | ASN | LEU | TYR | PHE | GLN | ||||
| 3 | GLY | HIS | PRO | LYS | ILE | MET | LYS | VAL | THR | VAL | ||||
| 4 | LYS | THR | PRO | LYS | GLU | LYS | GLU | GLU | PHE | ALA | ||||
| 5 | VAL | PRO | GLU | ASN | SER | SER | VAL | GLN | GLN | PHE | ||||
| 6 | LYS | GLU | GLU | ILE | SER | LYS | ARG | PHE | LYS | SER | ||||
| 7 | HIS | THR | ASP | GLN | LEU | VAL | LEU | ILE | PHE | ALA | ||||
| 8 | GLY | LYS | ILE | LEU | LYS | ASP | GLN | ASP | THR | LEU | ||||
| 9 | SER | GLN | HIS | GLY | ILE | HIS | ASP | GLY | LEU | THR | ||||
| 10 | VAL | HIS | LEU | VAL | ILE | LYS | THR | GLN | ASN | ARG | ||||
| 11 | PRO |
Samples:
sample_1: ubiquilin_1, [U-13C; U-15N], 0.5 mM; TRIS 10 mM; sodium chloride (NaCl) 300 mM; sodium azide (NaN3) 0.01%; inhibitor cocktail (roche) 1 x; benzamidine 1 mM; ZnSO4 10 uM; DTT 10 mM; D20 10%; H20 90%
sample_conditions_1: ionic strength: 300 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C_arom NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15 HSQC (IPAP) | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C Constant Time HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO (IPAP) | sample_1 | anisotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
FMC, Lemak, Steren, Llinas & Arrowsmith - chemical shift assignment
TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - data analysis
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
CNSSOLVE v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
TOPSPIN, Bruker Biospin - collection
PSVS v1.3, Bhattacharya and Montelione - validation
SPARKY v3.106, Goddard - peak picking
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz
Related Database Links:
| PDB | |
| DBJ | BAC33666 BAG51344 BAG51350 BAI46894 |
| EMBL | CAB66578 CAH92732 |
| GB | AAD49751 AAG02473 AAH10066 AAH39294 AAI20032 |
| REF | NP_001127579 NP_001155358 NP_038466 NP_444295 NP_777053 |
| SP | Q5R684 Q9UMX0 |
| TPG | DAA26626 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts