Ternary complex of an Crk SH2 domain, Crk-derived phophopeptide, and Abl SH3 domain by NMR spectroscopy
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_13C-separated_NOESY | 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide | 90% H2O/10% D2O | 50mM sodium phosphate | 6.8 | ambient | 303 | |
| 2 | 3D_15N-separated_NOESY | 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide | 90% H2O/10% D2O | 50mM sodium phosphate | 6.8 | ambient | 303 | |
| 3 | 3D_13C_F1-FILTERED_F3-EDITED_NOESY | 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide | 90% H2O/10% D2O | 50mM sodium phosphate | 6.8 | ambient | 303 | |
| 4 | J-HNHA | 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide | 90% H2O/10% D2O | 50mM sodium phosphate | 6.8 | ambient | 303 | |
| 5 | IPAP-15N_HSQC | 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide | 90% H2O/10% D2O | 50mM sodium phosphate | 6.8 | ambient | 303 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | UNITYPLUS | 500 |
| 2 | Varian | UNITYPLUS | 600 |
| 3 | Varian | UNITYPLUS | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| ARIA 1.0, CNS 1.0 | This structure represents the lowest energy solution based on 2406 SH2 intramolecular restraints, 1628 SH3 intramolecular restraints, 37 SH2-SH3 intermolecular restraints, 64 SH2-phosphopeptide intermolecular restraints, 50 hydrogen bonds, 54 direct 3J-HNHA couplings and 166 dihedral angle restraints from TALOS Residues 217-220 and 225-229 of the Crk phosphopeptide (Chain B) are disordered. As intermolecular contacts between the SH2 domain (Chain A) and the SH3 domain (Chain C) limited to amino acids 67-75 in DE-loop of the SH2 domain, there is no unique orientation between the SH2 domain and SH3 domain. | NMRPipe |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 40 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | Intermolecular distance restraints were obtained from reverse half-filtered 2D- and 3D-NOESY spectra (300 ms mixing time) on sample in 99% D2O. Methyl prochiral assignments were made on a 10% 13C-labeled sample according to Neri et al (Biochemistry 28:7510; 1989). HACAN and CBCA(CO)N(CA)HA experiments were used to assign the proline residues in the Crk SH2 domain according to Kanelis et al (JBNMR 16:253; 2000) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | NMRPipe | 1.8 | Delaglio |
| 2 | data analysis | PIPP | 4.3.2 | Garrett |
| 3 | structure solution | CNS | 1.0 | Brunger |
| 4 | structure solution | ARIA | 1.0 | Brunger |
| 5 | refinement | ARIA | 1.0 | Brunger |
