BMRB Entry 17239
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17239
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Title: NMR structure of the UBA domain of S. cerevisiae Dcn1 bound to ubiquitin
Deposition date: 2010-10-05 Original release date: 2012-07-25
Authors: Burschowsky, Daniel; Mattle, Daniel; Rudolf, Fabian; Peter, Matthias; Wider, Gerhard
Citation: Burschowsky, Daniel; Rudolf, Fabian; Mattle, Daniel; Peter, Matthias; Wider, Gerhard. "Structural analysis of the ubiquitin-associated domain (UBA) of yeast Dcn1 in complex with ubiquitin (WORKING TITLE)" Not known ., .-..
Assembly members:
Dcn1-UBA, polymer, 59 residues, 6780.567 Da.
ubiquitin, polymer, 76 residues, 8564.8 Da.
Natural source: Common Name: baker Taxonomy ID: 4932 Superkingdom: not available Kingdom: not available Genus/species: Eukaryota Fungi
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Dcn1-UBA: GSIKRKDASPEQEAIESFTS
LTKCDPKVSRKYLQRNHWNI
NYALNDYYDKEIGTFTDEV
ubiquitin: MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 201 |
| 15N chemical shifts | 65 |
| 1H chemical shifts | 419 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | UBA | 1 |
| 2 | ubi | 2 |
Entities:
Entity 1, UBA 59 residues - 6780.567 Da.
N-terminal residues number 4 and 5 (GS) are non-native and leftovers from thrombin cleavage
| 1 | GLY | SER | ILE | LYS | ARG | LYS | ASP | ALA | SER | PRO | ||||
| 2 | GLU | GLN | GLU | ALA | ILE | GLU | SER | PHE | THR | SER | ||||
| 3 | LEU | THR | LYS | CYS | ASP | PRO | LYS | VAL | SER | ARG | ||||
| 4 | LYS | TYR | LEU | GLN | ARG | ASN | HIS | TRP | ASN | ILE | ||||
| 5 | ASN | TYR | ALA | LEU | ASN | ASP | TYR | TYR | ASP | LYS | ||||
| 6 | GLU | ILE | GLY | THR | PHE | THR | ASP | GLU | VAL |
Entity 2, ubi 76 residues - 8564.8 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 | GLY |
Samples:
UBA-13C15N+Ub: Dcn1-UBA, [U-80% 13C; U-90% 15N], 0.8 mM; sodium chloride 15 mM; potassium phosphate 110 mM; DTT 2 mM; CHAPS 2 mM; sodium azide 0.02%; sodium chloride 25 mM; ubiquitin 3.2 mM; H2O 95%; D2O 5%
UBA-15N+Ub: Dcn1-UBA, [U-90% 15N], 0.5 mM; sodium phosphate 15 mM; potassium phosphate 110 mM; DTT 2 mM; CHAPS 2 mM; sodium azide 0.02%; sodium chloride 25 mM; ubiquitin 2 mM; H2O 95%; D2O 5%
NMR_Standard_Conditions: ionic strength: 182 mM; pH: 6.15; pressure: 1 atm; temperature: 288 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HCCH-COSY | UBA-13C15N+Ub | isotropic | NMR_Standard_Conditions |
| 3D HNCA | UBA-13C15N+Ub | isotropic | NMR_Standard_Conditions |
| 3D 1H-13C NOESY | UBA-13C15N+Ub | isotropic | NMR_Standard_Conditions |
| 3D 1H-13Caro NOESY | UBA-13C15N+Ub | isotropic | NMR_Standard_Conditions |
| 3D 1H-15N TOCSY | UBA-15N+Ub | isotropic | NMR_Standard_Conditions |
| 3D HNHB | UBA-15N+Ub | isotropic | NMR_Standard_Conditions |
| 3D 1H-15N NOESY | UBA-15N+Ub | isotropic | NMR_Standard_Conditions |
Software:
UNIO v1.0.4, Herrmann - chemical shift assignment, peak picking
AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement
CYANA v2, Guntert, Mumenthaler and Wuthrich - structure solution
TOPSPIN v2.0, Bruker Biospin - processing
CARA v1.8.4, Keller - data analysis
NMR spectrometers:
- Bruker Avance 700 MHz
- Bruker Avance 750 MHz
- Bruker Avance 900 MHz
Related Database Links:
| BMRB | 17238 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16880 16885 16895 17059 17181 17333 17439 17769 17919 18582 18583 18584 18610 18611 18737 19394 19399 19406 19412 19447 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111 |
| PDB | |
| DBJ | GAA25010 BAA03983 BAA09860 BAA11842 BAA11843 BAA23486 |
| EMBL | CAA61706 CAA62639 CAA97697 CAY81363 CAA25706 CAA26488 CAA28495 CAA30183 CAA30815 |
| GB | AAB82374 AHY78522 AJP40299 AJV46201 AJV46655 AAA02769 AAA28154 AAA28997 AAA28998 AAA28999 |
| REF | NP_013229 NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286 |
| SP | Q12395 P0C273 P0C275 P0C276 P0CG47 P0CG48 |
| TPG | DAA09439 DAA18802 DAA20663 DAA20672 DAA24675 DAA28295 |
| PIR | I50437 I51568 I65237 JN0790 S13928 |
| PRF | 0412265A 1101405A 1212243A 1212243B 1212243C |
| TPD | FAA00319 |
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