BMRB Entry 18737
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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/BMR18737
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Title: DISTINCT UBIQUITIN BINDING MODES EXHIBITED BY SH3 DOMAINS: M DETERMINANTS AND FUNCTIONAL IMPLICATIONS PubMed: 24039852
Deposition date: 2012-09-24 Original release date: 2013-09-30
Authors: Ortega-Roldan, J.; Azuaga, A.; Blackledge, M.; Van Nuland, N.
Citation: Ortega-Roldan, Jose; Casares, Salvador; Ringkjobing-Jensen, Malene; Cardenes, Nayra; Bravo, Jeronimo; Blackledge, Martin; Azuaga, Ana; Van Nuland, Nico. "Distinct Ubiquitin Binding Modes Exhibited by SH3 domains. Molecular Determinants and Functional Implications" PLoS One 8, e73018-e73018 (2013).
Assembly members:
UBIQUITIN, polymer, 76 residues, 8576.914 Da.
CD2-ASSOCIATED_PROTEIN, polymer, 63 residues, 6830.602 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):
UBIQUITIN: MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
CD2-ASSOCIATED_PROTEIN: AMGAKEYCRTLFPYTGTNED
ELTFREGEIIHLISKETGEA
GWWKGELNGKEGVFPDNFAV
QIS
- assigned_chemical_shifts
| Data type | Count |
| 15N chemical shifts | 133 |
| 1H chemical shifts | 133 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | UBIQUITIN | 1 |
| 2 | CD2-ASSOCIATED PROTEIN | 2 |
Entities:
Entity 1, 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 |
Entity 2, CD2-ASSOCIATED PROTEIN 63 residues - 6830.602 Da.
| 1 | ALA | MET | GLY | ALA | LYS | GLU | TYR | CYS | ARG | THR | ||||
| 2 | LEU | PHE | PRO | TYR | THR | GLY | THR | ASN | GLU | ASP | ||||
| 3 | GLU | LEU | THR | PHE | ARG | GLU | GLY | GLU | ILE | ILE | ||||
| 4 | HIS | LEU | ILE | SER | LYS | GLU | THR | GLY | GLU | ALA | ||||
| 5 | GLY | TRP | TRP | LYS | GLY | GLU | LEU | ASN | GLY | LYS | ||||
| 6 | GLU | GLY | VAL | PHE | PRO | ASP | ASN | PHE | ALA | VAL | ||||
| 7 | GLN | ILE | SER |
Samples:
sample_1: CD2AP SH3-C, [U-99% 15N], 0.2 mM; Ubiquitin 1 mM; H2O 90%; D2O 10%
sample_2: Ubiquitin, [U-99% 15N], 0.25 mM; CD2AP SH3-C 1 mM; H2O 90%; D2O 10%
sample_3: CD2AP SH3-C, [U-99% 13C; U-99% 15N], 0.9 mM; Ubiquitin, [U-99% 15N], 0.46 mM; H2O 90%; D2O 10%
sample_4: CD2AP SH3-C, [U-99% 13C; U-99% 15N], 0.828 mM; Ubiquitin, [U-99% 15N], 1.37 mM; H2O 90%; D2O 10%
sample_5: CD2AP SH3-C, [U-99% 13C; U-99% 15N], 0.78 mM; Ubiquitin, [U-99% 15N], 1.75 mM; H2O 90%; D2O 10%
sample_6: CD2AP SH3-C, [U-99% 13C; U-99% 15N], 0.25 mM; Ubiquitin, [U-99% 15N], 1.75 mM; H2O 90%; D2O 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, DOMINGUEZ, BOELENS - refinement, structure solution
CNS/SCULPTOR, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
NMRView, Johnson, One Moon Scientific - structure solution
NMR spectrometers:
- VARIAN UNIFORM NMR SYSTEM 600 MHz
- Varian Uniform NMR System 800 MHz
Related Database Links:
| BMRB | 11505 11547 15047 15410 15689 15907 16228 16582 16626 16895 17181 17439 17769 17919 18582 18583 18584 18610 18611 19406 19412 25070 25123 25601 26604 4245 4375 15407 16643 |
| PDB | |
| DBJ | BAA03983 BAA09860 BAA11842 BAA11843 BAA23486 |
| EMBL | CAA25706 CAA26488 CAA28495 CAA30183 CAA30815 |
| GB | AAA02769 AAA28154 AAA28997 AAA28998 AAA28999 |
| 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 |
| TPE | CEL68433 CEL70397 CEL75964 CEL78064 |
| 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