BMRB Entry 19447
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19447
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Title: DISTINCT UBIQUITIN BINDING MODES EXHIBITED BY SH3 DOMAINS: MOLECULAR DETERMINANTS AND FUNCTIONAL IMPLICATIONS PubMed: 24039852
Deposition date: 2013-08-22 Original release date: 2014-02-03
Authors: Ortega-Roldan, J.; Salmon, L.; Azuaga, A.; Blackledge, M.; Van Nuland, N.
Citation: Ortega-Roldan, J.; Casares, S.; Ringkjobing-Jensen, M.; Cardenes, N.; Bravo, N.; Blackledge, M.; Azuaga, A.; Van Nuland, N.. "Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications" PLoS One 8, e73018-e73018 (2013).
Assembly members:
SH3A, polymer, 61 residues, 6764.630 Da.
Ubiquitin, polymer, 76 residues, 8576.914 Da.
Natural source: Common Name: house mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
SH3A: VDYIVEYDYDAVHDDELTIR
VGEIIRNVKKLQEEGWLEGE
LNGRRGMFPDNFVKEIKRET
E
Ubiquitin: MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
- assigned_chemical_shifts
| Data type | Count |
| 15N chemical shifts | 132 |
| 1H chemical shifts | 132 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | SH3A | 1 |
| 2 | Ubiquitin | 2 |
Entities:
Entity 1, SH3A 61 residues - 6764.630 Da.
| 1 | VAL | ASP | TYR | ILE | VAL | GLU | TYR | ASP | TYR | ASP | ||||
| 2 | ALA | VAL | HIS | ASP | ASP | GLU | LEU | THR | ILE | ARG | ||||
| 3 | VAL | GLY | GLU | ILE | ILE | ARG | ASN | VAL | LYS | LYS | ||||
| 4 | LEU | GLN | GLU | GLU | GLY | TRP | LEU | GLU | GLY | GLU | ||||
| 5 | LEU | ASN | GLY | ARG | ARG | GLY | MET | PHE | PRO | ASP | ||||
| 6 | ASN | PHE | VAL | LYS | GLU | ILE | LYS | ARG | GLU | THR | ||||
| 7 | GLU |
Entity 2, Ubiquitin 76 residues - 8576.914 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:
sample_1: CD2AP SH3-A, [U-99% 15N], 0.2 mM; Ubiquitin 1 mM; H2O 90%; D2O, [U-100% 2H], 10%
sample_2: CD2AP SH3-A mM; Ubiquitin, [U-99% 15N], 0.25 mM; H2O 90%; D2O, [U-100% 2H], 10%
sample_3: CD2AP SH3-A, [U-99% 13C; U-99% 15N], 0.9 mM; Ubiquitin, [U-99% 15N], 0.46 mM; H2O 90%; D2O, [U-100% 2H], 10%
sample_4: CD2AP SH3-A, [U-99% 13C; U-99% 15N], 0.8 mM; Ubiquitin, [U-99% 15N], 1.37 mM; H2O 90%; D2O, [U-100% 2H], 10%
sample_5: CD2AP SH3-A, [U-99% 13C; U-99% 15N], 0.7 mM; Ubiquitin, [U-99% 15N], 1.75 mM; H2O 90%; D2O, [U-100% 2H], 10%
sample_6: CD2AP SH3-A, [U-99% 13C; U-99% 15N], 0.25 mM; Ubiquitin, [U-99% 15N], 1.75 mM; H2O 90%; D2O, [U-100% 2H], 10%
sample_conditions_1: ionic strength: 0 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO JNH, JCC, JCH, JCAHA | sample_3 | anisotropic | sample_conditions_1 |
| 3D HNCO JNH, JCC, JCH, JCAHA | sample_4 | anisotropic | sample_conditions_1 |
| 3D HNCO JNH, JCC, JCH, JCAHA | sample_5 | anisotropic | sample_conditions_1 |
| 2D 1H-15N HSQC FILTERED DIPSAP | sample_6 | anisotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
Software:
HADDOCK vCNS/SCULPTOR, DOMINGUEZ, BOELENS - refinement
CNS/SCULPTOR, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
NMRView, Johnson, One Moon Scientific - structure solution
HADDOCK, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
NMR spectrometers:
- VARIAN UNIFORM NMR SYSTEM 600 MHz
- Varian Uniform NMR System 800 MHz
Related Database Links:
| BMRB | 16641 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16880 16885 16895 17059 17181 17239 17333 17439 17769 17919 18582 18583 18584 18610 18611 18737 19394 19399 19406 19412 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111 |
| PDB | |
| GB | ELW65647 AAA02769 AAA28154 AAA28997 AAA28998 AAA28999 |
| DBJ | BAA03983 BAA09860 BAA11842 BAA11843 BAA23486 |
| EMBL | CAA25706 CAA26488 CAA28495 CAA30183 CAA30815 |
| PIR | I50437 I51568 I65237 JN0790 S13928 |
| PRF | 0412265A 1101405A 1212243A 1212243B 1212243C |
| REF | NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286 |
| SP | P0C273 P0C275 P0C276 P0CG47 P0CG48 |
| TPD | FAA00319 |
| TPG | DAA18802 DAA20663 DAA20672 DAA24675 DAA28295 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts